rs4474353

Variant names:

• chr10-8701350-G-A
• rs4474353

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 0.266 in 152,074 control chromosomes in the GnomAD database, including 5,992 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 0.27 (5992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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: 0.266 AC: 40459 AN: 151956 Hom.: 5974 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.266 AC: 40494 AN: 152074 Hom.: 5992 Cov.: 32 AF XY: 0.269 AC XY: 20000 AN XY: 74344

African (AFR) AF: 0.127 AC: 5277 AN: 41508

American (AMR) AF: 0.317 AC: 4842 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1836 AN: 5172

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4826

European-Finnish (FIN) AF: 0.318 AC: 3364 AN: 10568

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21648 AN: 67958

Other (OTH) AF: 0.287 AC: 603 AN: 2104

Alfa AF: 0.300 Hom.: 4258

Bravo AF: 0.259

Asia WGS AF: 0.312 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.24
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4474353; hg19: chr10-8743313;