rs2436893

chr8-102562435-G-Achr8-102562435-G-Cchr8-102562435-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.512

Alfa AF: 0.534 Hom.: 29155

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2436893; hg19: chr8-103574663;