rs3758496

Variant names:

• chr10-47322104-G-A
• rs3758496

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 0.247 in 152,080 control chromosomes in the GnomAD database, including 6,328 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 (6328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 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: 0.246 AC: 37446 AN: 151962 Hom.: 6323 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00868

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.247 AC: 37492 AN: 152080 Hom.: 6328 Cov.: 32 AF XY: 0.243 AC XY: 18098 AN XY: 74346

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.00870

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.232

Alfa AF: 0.187 Hom.: 1950

Bravo AF: 0.257

Asia WGS AF: 0.158 AC: 550 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.030
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758496; hg19: chr10-48417258;