chr6-32801886-T-C

Position:

• chr6-32801886-T-C

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 0.336 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32801886T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.337

Alfa AF: 0.321 Hom.: 2017

Bravo AF: 0.330

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2219893; hg19: chr6-32769663;