8-102566646-T-G

Variant names:

• chr8-102566646-T-G
• rs2511714

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 0.406 in 152,002 control chromosomes in the GnomAD database, including 13,084 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 0.41 (13084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 20 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 = 0.465 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: 0.406 AC: 61671 AN: 151884 Hom.: 13074 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.406 AC: 61726 AN: 152002 Hom.: 13084 Cov.: 32 AF XY: 0.401 AC XY: 29798 AN XY: 74292

African (AFR) AF: 0.471 AC: 19500 AN: 41438

American (AMR) AF: 0.338 AC: 5162 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3466

East Asian (EAS) AF: 0.104 AC: 539 AN: 5178

South Asian (SAS) AF: 0.200 AC: 965 AN: 4818

European-Finnish (FIN) AF: 0.470 AC: 4966 AN: 10562

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27983 AN: 67954

Other (OTH) AF: 0.383 AC: 806 AN: 2106

Alfa AF: 0.394 Hom.: 22885

Bravo AF: 0.400

Asia WGS AF: 0.186 AC: 649 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	2.6
DANN	Benign	0.53
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2511714; hg19: chr8-103578874;