rs4129374

Variant names:

• chr6-3204445-C-A
• rs4129374

Your query was ambiguous. Multiple possible variants found:

• chr6-3204445-C-A
• chr6-3204445-C-G

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 0.687 in 151,850 control chromosomes in the GnomAD database, including 36,171 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 0.69 (36171 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

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 (NFE) allele frequency at 95% confidence interval = 0.719 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: 0.687 AC: 104237 AN: 151732 Hom.: 36140 Cov.: 30

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.687 AC: 104314 AN: 151850 Hom.: 36171 Cov.: 30 AF XY: 0.682 AC XY: 50588 AN XY: 74178

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.681

Alfa AF: 0.682 Hom.: 5023

Bravo AF: 0.692

Asia WGS AF: 0.510 AC: 1770 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	0.45
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129374; hg19: chr6-3204679;