chr8-35041874-T-A

Variant names:

• chr8-35041874-T-A
• rs10503974

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 0.249 in 152,152 control chromosomes in the GnomAD database, including 5,119 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 0.25 (5119 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 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: 0.249 AC: 37864 AN: 152034 Hom.: 5112 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.249 AC: 37903 AN: 152152 Hom.: 5119 Cov.: 32 AF XY: 0.254 AC XY: 18862 AN XY: 74354

African (AFR) AF: 0.131 AC: 5437 AN: 41510

American (AMR) AF: 0.286 AC: 4370 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5174

South Asian (SAS) AF: 0.330 AC: 1593 AN: 4828

European-Finnish (FIN) AF: 0.308 AC: 3260 AN: 10588

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19567 AN: 67990

Other (OTH) AF: 0.271 AC: 571 AN: 2108

Alfa AF: 0.269 Hom.: 730

Bravo AF: 0.239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.35
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10503974; hg19: chr8-34899392; COSMIC: COSV70887832;