dbSNP rs2280871: TMEM71:c.*544G>A (chr8-132710423-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001382403.1(TMEM71):c.*544G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 158,790 control chromosomes in the GnomAD database, including 9,970 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 9856 hom., cov: 33)

Exomes 𝑓: 0.14 ( 114 hom. )

Consequence

TMEM71
NM_001382403.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03

Publications

15 publications found

Variant links:

Genes affected

TMEM71 (HGNC:26572): (transmembrane protein 71) Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

TMEM71 links:

ENSG00000287095 (HGNC:):

ENSG00000287095 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382403.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TMEM71	NM_001382403.1	MANE Select	c.*544G>A	3_prime_UTR	Exon 10 of 10	NP_001369332.1	Q6P5X7-1
TMEM71	NM_001382397.1		c.*544G>A	3_prime_UTR	Exon 11 of 11	NP_001369326.1
TMEM71	NM_001382402.1		c.*544G>A	3_prime_UTR	Exon 11 of 11	NP_001369331.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TMEM71	ENST00000677595.1	MANE Select	c.*544G>A	3_prime_UTR	Exon 10 of 10	ENSP00000504388.1	Q6P5X7-1
TMEM71	ENST00000356838.7	TSL:1	c.*544G>A	3_prime_UTR	Exon 10 of 10	ENSP00000349296.3	Q6P5X7-2
TMEM71	ENST00000377901.8	TSL:1	c.*544G>A	3_prime_UTR	Exon 9 of 9	ENSP00000367133.4	Q6P5X7-3

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42534

AN:

151976

Hom.:

9825

Cov.:

show subpopulations

Gnomad AFR

AF:

0.637

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.166

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.0946

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.230

GnomAD4 exome

AF:

0.144

AC:

966

AN:

6696

Hom.:

114

Cov.:

AF XY:

0.143

AC XY:

487

AN XY:

3410

show subpopulations

African (AFR)

AF:

0.606

AC:

132

AN:

218

American (AMR)

AF:

0.134

AC:

AN:

194

Ashkenazi Jewish (ASJ)

AF:

0.178

AC:

AN:

270

East Asian (EAS)

AF:

0.336

AC:

AN:

238

South Asian (SAS)

AF:

0.155

AC:

AN:

110

European-Finnish (FIN)

AF:

0.0826

AC:

AN:

230

Middle Eastern (MID)

AF:

0.222

AC:

AN:

European-Non Finnish (NFE)

AF:

0.112

AC:

552

AN:

4928

Other (OTH)

AF:

0.178

AC:

AN:

472

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

108

144

180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.280

AC:

42609

AN:

152094

Hom.:

9856

Cov.:

AF XY:

0.276

AC XY:

20487

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.637

AC:

26434

AN:

41466

American (AMR)

AF:

0.165

AC:

2529

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

770

AN:

3466

East Asian (EAS)

AF:

0.305

AC:

1577

AN:

5176

South Asian (SAS)

AF:

0.146

AC:

707

AN:

4826

European-Finnish (FIN)

AF:

0.0946

AC:

1001

AN:

10582

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.130

AC:

8842

AN:

67976

Other (OTH)

AF:

0.228

AC:

480

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1199

2398

3596

4795

5994

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

380

760

1140

1520

1900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.179

Hom.:

16336

Bravo

AF:

0.303

Asia WGS

AF:

0.224

AC:

777

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.10

(source)

DANN

Benign

0.44

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over