rs2213585

chr6-32445373-G-Achr6-32445373-G-Cchr6-32445373-G-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 0.616 in 151,860 control chromosomes in the GnomAD database, including 29,180 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 0.62 (29180 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.722 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: 0.616 AC: 93498 AN: 151742 Hom.: 29161 Cov.: 30

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.616 AC: 93560 AN: 151860 Hom.: 29180 Cov.: 30 AF XY: 0.617 AC XY: 45804 AN XY: 74212

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.651

Alfa AF: 0.614 Hom.: 19749

Bravo AF: 0.627

Asia WGS AF: 0.693 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.1
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2213585; hg19: chr6-32413150;