rs4713460

Positions:

• chr6-31380021-G-A
• chr6-31380021-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 0.328 in 151,852 control chromosomes in the GnomAD database, including 8,615 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 (8615 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49782 AN: 151734 Hom.: 8609 Cov.: 30

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.328 AC: 49820 AN: 151852 Hom.: 8615 Cov.: 30 AF XY: 0.338 AC XY: 25096 AN XY: 74186

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.357

Alfa AF: 0.313 Hom.: 4454

Bravo AF: 0.327

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713460; hg19: chr6-31347798;