chr6-29301152-C-A

Variant names:

• chr6-29301152-C-A
• rs9257691
• ENST00000733278.1:n.246-10600G>T

Variant summary

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

The ENST00000733278.1(ENSG00000295863):​n.246-10600G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,952 control chromosomes in the GnomAD database, including 14,650 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 0.42 (14650 hom., cov: 32)
• Consequence: ENSG00000295863 ENST00000733278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 7 publications found

Genes affected

ENSG00000295863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375005	XR_926670.1	n.220-16192G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295863	ENST00000733278.1	n.246-10600G>T		intron_variant	Intron 2 of 2
ENSG00000295863	ENST00000733279.1	n.390-10600G>T		intron_variant	Intron 4 of 4
ENSG00000295863	ENST00000733280.1	n.267-10600G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63669 AN: 151832 Hom.: 14638 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.419 AC: 63685 AN: 151952 Hom.: 14650 Cov.: 32 AF XY: 0.421 AC XY: 31281 AN XY: 74268

African (AFR) AF: 0.232 AC: 9636 AN: 41452

American (AMR) AF: 0.405 AC: 6180 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1677 AN: 5166

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4816

European-Finnish (FIN) AF: 0.593 AC: 6235 AN: 10522

Middle Eastern (MID) AF: 0.493 AC: 142 AN: 288

European-Non Finnish (NFE) AF: 0.519 AC: 35257 AN: 67944

Other (OTH) AF: 0.406 AC: 859 AN: 2114

Alfa AF: 0.416 Hom.: 13082

Bravo AF: 0.394

Asia WGS AF: 0.405 AC: 1407 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.059
DANN	Benign	0.28
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs9257691; hg19: chr6-29268929;