7-81938641-A-T

Position:

• chr7-81938641-A-T

Variant summary

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

The variant allele was found at a frequency of 0.513 in 151,900 control chromosomes in the GnomAD database, including 20,142 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 0.51 (20142 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.81938641A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77929 AN: 151782 Hom.: 20126 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.513 AC: 77987 AN: 151900 Hom.: 20142 Cov.: 31 AF XY: 0.511 AC XY: 37971 AN XY: 74238

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.532

Alfa AF: 0.481 Hom.: 2101

Bravo AF: 0.519

Asia WGS AF: 0.454 AC: 1578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1229497; hg19: chr7-81567957;