rs4713462

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;