6-32445317-A-G

Variant names:

• chr6-32445317-A-G
• rs2213586

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 0.615 in 151,702 control chromosomes in the GnomAD database, including 29,065 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 (29065 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93290 AN: 151582 Hom.: 29045 Cov.: 30

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.615 AC: 93354 AN: 151702 Hom.: 29065 Cov.: 30 AF XY: 0.616 AC XY: 45694 AN XY: 74132

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.651

Alfa AF: 0.610 Hom.: 22434

Asia WGS AF: 0.669 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
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: rs2213586; hg19: chr6-32413094;