rs3104405

Positions:

• chr6-32714531-C-A
• chr6-32714531-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 0.649 in 151,884 control chromosomes in the GnomAD database, including 32,405 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 0.65 (32405 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32714531C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98508 AN: 151766 Hom.: 32393 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.649 AC: 98569 AN: 151884 Hom.: 32405 Cov.: 32 AF XY: 0.645 AC XY: 47849 AN XY: 74188

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.695

Alfa AF: 0.675 Hom.: 21241

Bravo AF: 0.663

Asia WGS AF: 0.790 AC: 2746 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3104405; hg19: chr6-32682308;