rs10505599

chr8-132730731-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001382403.1(TMEM71):c.488-2745T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,194 control chromosomes in the GnomAD database, including 1,260 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 0.11 (1260 hom., cov: 32)
• Consequence: TMEM71 NM_001382403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM71	NM_001382403.1	c.488-2745T>A		intron_variant		ENST00000677595.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM71	ENST00000677595.1	c.488-2745T>A		intron_variant			NM_001382403.1	P1
TMEM71	ENST00000356838.7	c.431-2745T>A		intron_variant		1
TMEM71	ENST00000377901.8	c.488-8616T>A		intron_variant		1
TMEM71	ENST00000523829.5	c.488-2745T>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16708 AN: 152076 Hom.: 1260 Cov.: 32

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0285

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.110 AC: 16706 AN: 152194 Hom.: 1260 Cov.: 32 AF XY: 0.108 AC XY: 8020 AN XY: 74412

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.0764

Gnomad4 ASJ AF: 0.0899

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.107

Alfa AF: 0.151 Hom.: 253

Bravo AF: 0.0999

Asia WGS AF: 0.0190 AC: 65 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	4.0
Dann	Benign	0.51

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

LitVar

Other links and lift over

dbSNP: rs10505599; hg19: chr8-133742977;