rs4736601

Variant names:

• chr8-132703898-C-T
• rs4736601
• ENST00000522780.5:c.264-16243G>A

Variant summary

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

The ENST00000522780.5(TMEM71):​c.264-16243G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,832 control chromosomes in the GnomAD database, including 27,664 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 0.57 (27664 hom., cov: 30)
• Consequence: TMEM71 ENST00000522780.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 5 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 = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM71	ENST00000522780.5	c.264-16243G>A		intron_variant	Intron 2 of 3	4		ENSP00000428772.1
ENSG00000287095	ENST00000666760.2	n.260+838C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86294 AN: 151714 Hom.: 27600 Cov.: 30

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.532

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.569 AC: 86412 AN: 151832 Hom.: 27664 Cov.: 30 AF XY: 0.563 AC XY: 41776 AN XY: 74174

African (AFR) AF: 0.882 AC: 36510 AN: 41418

American (AMR) AF: 0.396 AC: 6041 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1833 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3140 AN: 5118

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4812

European-Finnish (FIN) AF: 0.416 AC: 4377 AN: 10532

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30924 AN: 67914

Other (OTH) AF: 0.537 AC: 1133 AN: 2108

Alfa AF: 0.545 Hom.: 3233

Bravo AF: 0.583

Asia WGS AF: 0.518 AC: 1805 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	1.2
DANN	Benign	0.56
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4736601; hg19: chr8-133716144;