8-31587891-T-C

Variant names:

• chr8-31587891-T-C
• rs763552

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 0.51 in 151,932 control chromosomes in the GnomAD database, including 20,080 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 (20080 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.510 AC: 77396 AN: 151812 Hom.: 20062 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.510 AC: 77463 AN: 151932 Hom.: 20080 Cov.: 31 AF XY: 0.508 AC XY: 37693 AN XY: 74232

African (AFR) AF: 0.481 AC: 19939 AN: 41442

American (AMR) AF: 0.453 AC: 6912 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3466

East Asian (EAS) AF: 0.808 AC: 4159 AN: 5150

South Asian (SAS) AF: 0.581 AC: 2798 AN: 4814

European-Finnish (FIN) AF: 0.472 AC: 4975 AN: 10544

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34893 AN: 67940

Other (OTH) AF: 0.533 AC: 1125 AN: 2110

Alfa AF: 0.517 Hom.: 10765

Bravo AF: 0.506

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.28
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs763552; hg19: chr8-31445407;