8-102562435-G-A

Variant names:

• chr8-102562435-G-A
• rs2436893

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 0.483 in 151,904 control chromosomes in the GnomAD database, including 18,254 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 0.48 (18254 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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: 0.483 AC: 73376 AN: 151786 Hom.: 18241 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.483 AC: 73439 AN: 151904 Hom.: 18254 Cov.: 31 AF XY: 0.480 AC XY: 35656 AN XY: 74252

African (AFR) AF: 0.408 AC: 16908 AN: 41396

American (AMR) AF: 0.476 AC: 7256 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2111 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1140 AN: 5170

South Asian (SAS) AF: 0.382 AC: 1836 AN: 4810

European-Finnish (FIN) AF: 0.526 AC: 5543 AN: 10542

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

European-Non Finnish (NFE) AF: 0.543 AC: 36871 AN: 67942

Other (OTH) AF: 0.512 AC: 1080 AN: 2110

Alfa AF: 0.525 Hom.: 38995

Bravo AF: 0.474

Asia WGS AF: 0.353 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.68
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs2436893; hg19: chr8-103574663;