rs3758496

Variant names:

• chr10-47322104-G-A
• rs3758496

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 0.247 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.481 AC: 19936 AN: 41438

American (AMR) AF: 0.153 AC: 2344 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3468

East Asian (EAS) AF: 0.00870 AC: 45 AN: 5172

South Asian (SAS) AF: 0.203 AC: 981 AN: 4822

European-Finnish (FIN) AF: 0.152 AC: 1613 AN: 10594

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11385 AN: 67978

Other (OTH) AF: 0.232 AC: 489 AN: 2110

Alfa AF: 0.201 Hom.: 3242

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
PhyloP100		-3.2
PromoterAI		-0.033	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3758496; hg19: chr10-48417258;