6-32445540-G-T

Variant names:

• chr6-32445540-G-T
• rs2395182

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 0.768 in 152,088 control chromosomes in the GnomAD database, including 45,037 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 0.77 (45037 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.768 AC: 116768 AN: 151970 Hom.: 45021 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.768 AC: 116836 AN: 152088 Hom.: 45037 Cov.: 31 AF XY: 0.767 AC XY: 57010 AN XY: 74340

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.800

Alfa AF: 0.791 Hom.: 50331

Bravo AF: 0.774

Asia WGS AF: 0.783 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395182; hg19: chr6-32413317;