rs4474353

chr10-8701350-G-A

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 0.266 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.287

Alfa AF: 0.301 Hom.: 2636

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4474353; hg19: chr10-8743313;