rs3843561

Positions:

• chr8-132702241-G-A
• chr8-132702241-G-C

Variant summary

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

The XM_006716538.4(DNAAF11):​c.-426C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,070 control chromosomes in the GnomAD database, including 3,302 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 0.18 (3302 hom., cov: 32)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: DNAAF11 XM_006716538.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813

Genes affected

DNAAF11 (HGNC:):

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAAF11	XM_006716538.4	c.-426C>T		5_prime_UTR_variant	1/14		XP_006716601.2
DNAAF11	XM_011516950.3	c.-426C>T		5_prime_UTR_variant	1/13		XP_011515252.1
DNAAF11	XM_047421656.1	c.-426C>T		5_prime_UTR_variant	1/13		XP_047277612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM71	ENST00000522780.5	c.266-14586C>T		intron_variant		4		ENSP00000428772
TMEM71	ENST00000524079.5			upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27795 AN: 151930 Hom.: 3303 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.203

GnomAD4 exome AF: 0.136 AC: 3 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.183 AC: 27793 AN: 152048 Hom.: 3302 Cov.: 32 AF XY: 0.189 AC XY: 14078 AN XY: 74294

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.200

Alfa AF: 0.211 Hom.: 4677

Bravo AF: 0.178

Asia WGS AF: 0.290 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3843561; hg19: chr8-133714487;