ENST00000776319.1:n.339+24027G>A

Variant names:

• chr6-150552630-C-T
• rs7740233
• ENST00000776319.1:n.339+24027G>A

Variant summary

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

The ENST00000776319.1(ENSG00000301114):​n.339+24027G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 149,576 control chromosomes in the GnomAD database, including 24,078 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 0.56 (24078 hom., cov: 24)
• Consequence: ENSG00000301114 ENST00000776319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 4 publications found

Genes affected

ENSG00000301114 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301114	ENST00000776319.1	n.339+24027G>A		intron_variant	Intron 1 of 1
ENSG00000301114	ENST00000776320.1	n.126-748G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 84264 AN: 149458 Hom.: 24074 Cov.: 24

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.564 AC: 84300 AN: 149576 Hom.: 24078 Cov.: 24 AF XY: 0.567 AC XY: 41287 AN XY: 72834

African (AFR) AF: 0.551 AC: 22345 AN: 40540

American (AMR) AF: 0.483 AC: 7234 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1732 AN: 3462

East Asian (EAS) AF: 0.466 AC: 2326 AN: 4990

South Asian (SAS) AF: 0.641 AC: 3000 AN: 4682

European-Finnish (FIN) AF: 0.696 AC: 6976 AN: 10024

Middle Eastern (MID) AF: 0.490 AC: 141 AN: 288

European-Non Finnish (NFE) AF: 0.576 AC: 38939 AN: 67620

Other (OTH) AF: 0.509 AC: 1060 AN: 2084

Alfa AF: 0.565 Hom.: 95035

Bravo AF: 0.543

Asia WGS AF: 0.547 AC: 1901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7740233; hg19: chr6-150873766;