rs384662

chr5-35385570-A-Cchr5-35385570-A-Gchr5-35385570-A-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 0.924 in 152,000 control chromosomes in the GnomAD database, including 65,457 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 0.92 (65457 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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: 0.924 AC: 140332 AN: 151882 Hom.: 65421 Cov.: 29

Gnomad AFR AF: 0.801

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.924 AC: 140426 AN: 152000 Hom.: 65457 Cov.: 29 AF XY: 0.923 AC XY: 68572 AN XY: 74262

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.995

Gnomad4 OTH AF: 0.922

Alfa AF: 0.966 Hom.: 11715

Bravo AF: 0.908

Asia WGS AF: 0.914 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.3
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs384662; hg19: chr5-35385672;