6-32801886-T-C

Variant names:

• chr6-32801886-T-C
• rs2219893

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 0.336 in 151,904 control chromosomes in the GnomAD database, including 8,789 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 0.34 (8789 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 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: 0.336 AC: 51027 AN: 151786 Hom.: 8785 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.336 AC: 51050 AN: 151904 Hom.: 8789 Cov.: 32 AF XY: 0.343 AC XY: 25483 AN XY: 74244

African (AFR) AF: 0.292 AC: 12085 AN: 41426

American (AMR) AF: 0.394 AC: 6009 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1928 AN: 5166

South Asian (SAS) AF: 0.430 AC: 2074 AN: 4822

European-Finnish (FIN) AF: 0.428 AC: 4497 AN: 10518

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21958 AN: 67938

Other (OTH) AF: 0.337 AC: 709 AN: 2106

Alfa AF: 0.321 Hom.: 2735

Bravo AF: 0.330

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.39
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2219893; hg19: chr6-32769663;