dbSNP rs17121510: SMIM35:c.*970T>C (chr11-118005440-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001394165.1(SMIM35):c.*970T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,180 control chromosomes in the GnomAD database, including 1,929 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 0.15 ( 1927 hom., cov: 32)

Exomes 𝑓: 0.13 ( 2 hom. )

Consequence

SMIM35
NM_001394165.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.677

Publications

13 publications found

Variant links:

Genes affected

SMIM35 (HGNC:44179): (small integral membrane protein 35) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SMIM35 links:

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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=-0.69).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
SMIM35	NM_001394165.1 link	c.*970T>C	3_prime_UTR_variant	Exon 5 of 5	ENST00000689828.1	NP_001381094.1
SMIM35	NM_001394164.1 link	c.*970T>C	3_prime_UTR_variant	Exon 6 of 6		NP_001381093.1
SMIM35	NM_001394166.1 link	c.*970T>C	3_prime_UTR_variant	Exon 4 of 4		NP_001381095.1
SMIM35	XM_024448283.2 link	c.*970T>C	3_prime_UTR_variant	Exon 7 of 7		XP_024304051.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM35	ENST00000689828.1 link	c.*970T>C		3_prime_UTR_variant	Exon 5 of 5		NM_001394165.1	ENSP00000509259.1		A0A1B0GVV1
SMIM35	ENST00000636151.1 link	c.*1014T>C		3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000490666.1		A0A1B0GVV1

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22110

AN:

151970

Hom.:

1925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.0436

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.149

GnomAD4 exome

AF:

0.130

AC:

AN:

Hom.:

Cov.:

AF XY:

0.153

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0946

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.563

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.146

AC:

22137

AN:

152088

Hom.:

1927

Cov.:

AF XY:

0.145

AC XY:

10802

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.239

AC:

9894

AN:

41462

American (AMR)

AF:

0.120

AC:

1834

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

381

AN:

3468

East Asian (EAS)

AF:

0.0437

AC:

226

AN:

5168

South Asian (SAS)

AF:

0.104

AC:

500

AN:

4822

European-Finnish (FIN)

AF:

0.117

AC:

1233

AN:

10582

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.110

AC:

7460

AN:

67982

Other (OTH)

AF:

0.148

AC:

313

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

940

1880

2821

3761

4701

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.120

Hom.:

4120

Bravo

AF:

0.148

Asia WGS

AF:

0.0840

AC:

292

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

4.8

(source)

DANN

Benign

0.88

PhyloP100

-0.68

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over