rs10503973

Positions:

• chr8-35041744-C-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 0.25 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

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 (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.274

Alfa AF: 0.265 Hom.: 955

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503973; hg19: chr8-34899262;