6-32427879-A-T

Position:

• chr6-32427879-A-T

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 0.138 in 152,182 control chromosomes in the GnomAD database, including 1,663 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 0.14 (1663 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32427879A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20947 AN: 152064 Hom.: 1663 Cov.: 32

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.138 AC: 20955 AN: 152182 Hom.: 1663 Cov.: 32 AF XY: 0.136 AC XY: 10123 AN XY: 74410

Gnomad4 AFR AF: 0.0755

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0925

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.135

Alfa AF: 0.151 Hom.: 259

Bravo AF: 0.129

Asia WGS AF: 0.127 AC: 440 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2105903; hg19: chr6-32395656;