rs2280871

chr8-132710423-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM71	NM_001382403.1	c.*544G>A		3_prime_UTR_variant	10/10	ENST00000677595.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM71	ENST00000677595.1	c.*544G>A		3_prime_UTR_variant	10/10		NM_001382403.1	P1
	ENST00000666760.1	n.249+7363C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.606

Gnomad4 AMR exome AF: 0.134

Gnomad4 ASJ exome AF: 0.178

Gnomad4 EAS exome AF: 0.336

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.0826

Gnomad4 NFE exome AF: 0.112

Gnomad4 OTH exome AF: 0.178

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

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0946

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.228

Alfa AF: 0.159 Hom.: 5495

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

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: rs2280871; hg19: chr8-133722669;