rs10503975

Variant names:

• chr8-35043065-T-C
• rs10503975

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 152,124 control chromosomes in the GnomAD database, including 5,128 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 (5128 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 37889 AN: 152006 Hom.: 5122 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.249 AC: 37926 AN: 152124 Hom.: 5128 Cov.: 33 AF XY: 0.254 AC XY: 18881 AN XY: 74360

African (AFR) AF: 0.131 AC: 5453 AN: 41506

American (AMR) AF: 0.286 AC: 4375 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1265 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1359 AN: 5168

South Asian (SAS) AF: 0.331 AC: 1595 AN: 4826

European-Finnish (FIN) AF: 0.308 AC: 3250 AN: 10560

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

European-Non Finnish (NFE) AF: 0.288 AC: 19577 AN: 67996

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.264 Hom.: 737

Bravo AF: 0.239

Asia WGS AF: 0.315 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.73
DANN	Benign	0.44
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10503975; hg19: chr8-34900583;