7-81938641-A-T

Variant names:

• chr7-81938641-A-T
• rs1229497

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;