rs2280871

Variant names:

• chr8-132710423-C-T
• rs2280871
• NM_001382403.1:c.*544G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 15 publications found

Genes affected

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

ENSG00000287095 (HGNC:):

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM71	NM_001382403.1	c.*544G>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000677595.1	NP_001369332.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM71	ENST00000677595.1	c.*544G>A		3_prime_UTR_variant	Exon 10 of 10		NM_001382403.1	ENSP00000504388.1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42534 AN: 151976 Hom.: 9825 Cov.: 33

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.: 0 AF XY: 0.143 AC XY: 487 AN XY: 3410

African (AFR) AF: 0.606 AC: 132 AN: 218

American (AMR) AF: 0.134 AC: 26 AN: 194

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 48 AN: 270

East Asian (EAS) AF: 0.336 AC: 80 AN: 238

South Asian (SAS) AF: 0.155 AC: 17 AN: 110

European-Finnish (FIN) AF: 0.0826 AC: 19 AN: 230

Middle Eastern (MID) AF: 0.222 AC: 8 AN: 36

European-Non Finnish (NFE) AF: 0.112 AC: 552 AN: 4928

Other (OTH) AF: 0.178 AC: 84 AN: 472

GnomAD4 genome AF: 0.280 AC: 42609 AN: 152094 Hom.: 9856 Cov.: 33 AF XY: 0.276 AC XY: 20487 AN XY: 74342

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: 73 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8842 AN: 67976

Other (OTH) AF: 0.228 AC: 480 AN: 2108

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.44
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2280871; hg19: chr8-133722669;