8-612629-A-T

Variant names:

• chr8-612629-A-T
• rs1669703

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 0.536 in 152,092 control chromosomes in the GnomAD database, including 22,058 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 0.54 (22058 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

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 = 0.589 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: 0.535 AC: 81367 AN: 151974 Hom.: 22018 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.536 AC: 81459 AN: 152092 Hom.: 22058 Cov.: 33 AF XY: 0.538 AC XY: 40024 AN XY: 74348

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.548

Alfa AF: 0.346 Hom.: 806

Bravo AF: 0.545

Asia WGS AF: 0.551 AC: 1914 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	1.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1669703; hg19: chr8-562629;