6-32774091-T-C

Variant names:

• chr6-32774091-T-C
• rs2621416

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 0.259 in 152,072 control chromosomes in the GnomAD database, including 5,459 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 0.26 (5459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39313 AN: 151954 Hom.: 5450 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.259 AC: 39358 AN: 152072 Hom.: 5459 Cov.: 32 AF XY: 0.266 AC XY: 19781 AN XY: 74308

African (AFR) AF: 0.172 AC: 7150 AN: 41520

American (AMR) AF: 0.305 AC: 4658 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1954 AN: 5172

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4082 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18161 AN: 67940

Other (OTH) AF: 0.249 AC: 525 AN: 2110

Alfa AF: 0.268 Hom.: 19430

Bravo AF: 0.253

Asia WGS AF: 0.344 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.44
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2621416; hg19: chr6-32741868;