chr6-32427879-A-T

Variant names:

• chr6-32427879-A-T
• rs2105903
• ENST00000766247.1:n.283-6213A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000766247.1(ENSG00000299769):​n.283-6213A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 14 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766247.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299769	ENST00000766247.1		n.283-6213A>T		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.391+2407A>T		intron	N/A

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

African (AFR) AF: 0.0755 AC: 3136 AN: 41538

American (AMR) AF: 0.117 AC: 1792 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3466

East Asian (EAS) AF: 0.127 AC: 659 AN: 5182

South Asian (SAS) AF: 0.0925 AC: 446 AN: 4824

European-Finnish (FIN) AF: 0.205 AC: 2165 AN: 10566

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11996 AN: 67982

Other (OTH) AF: 0.135 AC: 285 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.68
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2105903; hg19: chr6-32395656;