6-32251264-C-T

Variant names:

• chr6-32251264-C-T
• rs6916062

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 0.0376 in 152,010 control chromosomes in the GnomAD database, including 131 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 0.038 (131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0519 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: 0.0376 AC: 5705 AN: 151892 Hom.: 131 Cov.: 31

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00888

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0381

Gnomad OTH AF: 0.0336

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

GnomAD4 genome AF: 0.0376 AC: 5708 AN: 152010 Hom.: 131 Cov.: 31 AF XY: 0.0362 AC XY: 2688 AN XY: 74308

African (AFR) AF: 0.0508 AC: 2104 AN: 41440

American (AMR) AF: 0.0185 AC: 283 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3470

East Asian (EAS) AF: 0.00890 AC: 46 AN: 5170

South Asian (SAS) AF: 0.0574 AC: 276 AN: 4806

European-Finnish (FIN) AF: 0.0133 AC: 140 AN: 10564

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0381 AC: 2592 AN: 67984

Other (OTH) AF: 0.0332 AC: 70 AN: 2108

Alfa AF: 0.0335 Hom.: 180

Bravo AF: 0.0384

Asia WGS AF: 0.0220 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.83
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6916062; hg19: chr6-32219041;