chr8-63087002-A-T

Variant names:

• chr8-63087002-A-T
• rs6994076

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 0.575 in 152,116 control chromosomes in the GnomAD database, including 25,969 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 0.58 (25969 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 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: 0.575 AC: 87432 AN: 151996 Hom.: 25926 Cov.: 33

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.575 AC: 87528 AN: 152116 Hom.: 25969 Cov.: 33 AF XY: 0.584 AC XY: 43433 AN XY: 74364

African (AFR) AF: 0.694 AC: 28819 AN: 41512

American (AMR) AF: 0.601 AC: 9189 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1774 AN: 3472

East Asian (EAS) AF: 0.772 AC: 3985 AN: 5160

South Asian (SAS) AF: 0.615 AC: 2964 AN: 4816

European-Finnish (FIN) AF: 0.612 AC: 6476 AN: 10586

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32693 AN: 67976

Other (OTH) AF: 0.553 AC: 1167 AN: 2112

Alfa AF: 0.547 Hom.: 2880

Bravo AF: 0.579

Asia WGS AF: 0.675 AC: 2345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.45
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs6994076; hg19: chr8-63999561;