6-32805395-C-T

Variant names:

• chr6-32805395-C-T
• rs2199870

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 0.672 in 151,792 control chromosomes in the GnomAD database, including 34,469 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 0.67 (34469 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.787 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: 0.672 AC: 101905 AN: 151676 Hom.: 34462 Cov.: 30

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.672 AC: 101948 AN: 151792 Hom.: 34469 Cov.: 30 AF XY: 0.679 AC XY: 50333 AN XY: 74168

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.682

Alfa AF: 0.661 Hom.: 18353

Bravo AF: 0.657

Asia WGS AF: 0.749 AC: 2605 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.85
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2199870; hg19: chr6-32773172;