rs4713580

Positions:

• chr6-32692217-C-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 0.536 in 151,954 control chromosomes in the GnomAD database, including 22,307 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 0.54 (22307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 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: 0.536 AC: 81431 AN: 151836 Hom.: 22286 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.536 AC: 81508 AN: 151954 Hom.: 22307 Cov.: 31 AF XY: 0.541 AC XY: 40182 AN XY: 74282

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.555

Alfa AF: 0.526 Hom.: 3129

Bravo AF: 0.543

Asia WGS AF: 0.596 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	12
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713580; hg19: chr6-32659994;