8-612629-A-T

Variant names:

• chr8-612629-A-T
• rs1669703

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.595 AC: 24696 AN: 41506

American (AMR) AF: 0.583 AC: 8912 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2429 AN: 5162

South Asian (SAS) AF: 0.565 AC: 2717 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5442 AN: 10574

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33223 AN: 67968

Other (OTH) AF: 0.548 AC: 1156 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1669703; hg19: chr8-562629;