rs10034579

Variant names:

• chr4-119322874-A-C
• rs10034579

Your query was ambiguous. Multiple possible variants found:

• chr4-119322874-A-C
• chr4-119322874-A-G
• chr4-119322874-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 0.567 in 151,982 control chromosomes in the GnomAD database, including 24,451 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 0.57 (24451 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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: 0.567 AC: 86072 AN: 151864 Hom.: 24418 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.567 AC: 86171 AN: 151982 Hom.: 24451 Cov.: 32 AF XY: 0.564 AC XY: 41918 AN XY: 74314

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.599

Alfa AF: 0.478 Hom.: 1843

Bravo AF: 0.579

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10034579; hg19: chr4-120244029;