rs603979

Variant names:

• chr5-41576232-G-A
• rs603979

Your query was ambiguous. Multiple possible variants found:

• chr5-41576232-G-A
• chr5-41576232-G-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 0.103 in 152,032 control chromosomes in the GnomAD database, including 969 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 0.10 (969 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.103 AC: 15675 AN: 151914 Hom.: 967 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.0639

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15678 AN: 152032 Hom.: 969 Cov.: 33 AF XY: 0.100 AC XY: 7465 AN XY: 74304

African (AFR) AF: 0.178 AC: 7376 AN: 41440

American (AMR) AF: 0.0844 AC: 1289 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3468

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5172

South Asian (SAS) AF: 0.0631 AC: 304 AN: 4816

European-Finnish (FIN) AF: 0.0472 AC: 499 AN: 10566

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0803 AC: 5460 AN: 67984

Other (OTH) AF: 0.110 AC: 231 AN: 2104

Alfa AF: 0.0525 Hom.: 53

Bravo AF: 0.110

Asia WGS AF: 0.0490 AC: 172 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.064
DANN	Benign	0.61
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs603979; hg19: chr5-41576334;