rs4713462

Variant names:

• chr6-31380039-G-A
• rs4713462

Your query was ambiguous. Multiple possible variants found:

• chr6-31380039-G-A
• chr6-31380039-G-C

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 0.327 in 151,804 control chromosomes in the GnomAD database, including 8,603 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 0.33 (8603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 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: 0.327 AC: 49546 AN: 151686 Hom.: 8595 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.327 AC: 49586 AN: 151804 Hom.: 8603 Cov.: 31 AF XY: 0.337 AC XY: 24973 AN XY: 74176

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.355

Alfa AF: 0.312 Hom.: 5797

Bravo AF: 0.327

Asia WGS AF: 0.523 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713462; hg19: chr6-31347816;