rs384662

Variant names:

• chr5-35385570-A-C
• rs384662

Your query was ambiguous. Multiple possible variants found:

• chr5-35385570-A-C
• chr5-35385570-A-G
• chr5-35385570-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;