rs10503973

Variant names:

• chr8-35041744-C-T
• rs10503973

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 0.25 in 152,068 control chromosomes in the GnomAD database, including 5,136 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 (5136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 3 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 (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: 0.250 AC: 37913 AN: 151950 Hom.: 5129 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.250 AC: 37952 AN: 152068 Hom.: 5136 Cov.: 32 AF XY: 0.254 AC XY: 18888 AN XY: 74350

African (AFR) AF: 0.132 AC: 5464 AN: 41502

American (AMR) AF: 0.288 AC: 4401 AN: 15276

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

East Asian (EAS) AF: 0.264 AC: 1362 AN: 5152

South Asian (SAS) AF: 0.330 AC: 1591 AN: 4816

European-Finnish (FIN) AF: 0.308 AC: 3256 AN: 10580

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19563 AN: 67964

Other (OTH) AF: 0.274 AC: 578 AN: 2112

Alfa AF: 0.261 Hom.: 962

Bravo AF: 0.240

Asia WGS AF: 0.316 AC: 1098 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.76
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10503973; hg19: chr8-34899262;