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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.801 AC: 33158 AN: 41418

American (AMR) AF: 0.881 AC: 13453 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3459 AN: 3472

East Asian (EAS) AF: 0.833 AC: 4261 AN: 5118

South Asian (SAS) AF: 0.977 AC: 4699 AN: 4810

European-Finnish (FIN) AF: 0.999 AC: 10583 AN: 10598

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67680 AN: 68004

Other (OTH) AF: 0.922 AC: 1936 AN: 2100

Alfa AF: 0.956 Hom.: 32979

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs384662; hg19: chr5-35385672;