chr6-32408969-C-T

Variant names:

• chr6-32408969-C-T
• rs3763316

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 0.239 in 152,076 control chromosomes in the GnomAD database, including 4,590 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 0.24 (4590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.288 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: 0.240 AC: 36408 AN: 151958 Hom.: 4591 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.239 AC: 36422 AN: 152076 Hom.: 4590 Cov.: 32 AF XY: 0.236 AC XY: 17510 AN XY: 74332

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.231

Alfa AF: 0.265 Hom.: 7524

Bravo AF: 0.253

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763316; hg19: chr6-32376746;