chr6-32610305-C-T

Variant names:

• chr6-32610305-C-T
• rs674313

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.294 in 152,062 control chromosomes in the GnomAD database, including 7,081 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 0.29 (7081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 68 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 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: 0.294 AC: 44695 AN: 151944 Hom.: 7074 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.294 AC: 44737 AN: 152062 Hom.: 7081 Cov.: 32 AF XY: 0.291 AC XY: 21640 AN XY: 74344

African (AFR) AF: 0.387 AC: 16026 AN: 41424

American (AMR) AF: 0.261 AC: 3982 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1649 AN: 5182

South Asian (SAS) AF: 0.263 AC: 1268 AN: 4824

European-Finnish (FIN) AF: 0.216 AC: 2288 AN: 10590

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17547 AN: 67974

Other (OTH) AF: 0.313 AC: 661 AN: 2112

Alfa AF: 0.275 Hom.: 14412

Bravo AF: 0.301

Asia WGS AF: 0.258 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.85
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs674313; hg19: chr6-32578082;