ENST00000776537.1:n.238+13772C>G

Variant names:

• chr17-34238101-G-C
• rs758294
• ENST00000776537.1:n.238+13772C>G

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+13772C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,234 control chromosomes in the GnomAD database, including 58,017 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 0.87 (58017 hom., cov: 32)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687
• Publications: 3 publications found

Genes affected

ENSG00000301139 (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 (AFR) allele frequency at 95% confidence interval = 0.954 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
ENSG00000301139	ENST00000776537.1	n.238+13772C>G		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.238+13772C>G		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.236+13772C>G		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776540.1	n.158+13772C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132423 AN: 152116 Hom.: 57951 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.871 AC: 132551 AN: 152234 Hom.: 58017 Cov.: 32 AF XY: 0.874 AC XY: 65070 AN XY: 74426

African (AFR) AF: 0.962 AC: 39956 AN: 41546

American (AMR) AF: 0.878 AC: 13438 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2911 AN: 3470

East Asian (EAS) AF: 0.929 AC: 4805 AN: 5170

South Asian (SAS) AF: 0.917 AC: 4419 AN: 4820

European-Finnish (FIN) AF: 0.839 AC: 8898 AN: 10600

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55515 AN: 68010

Other (OTH) AF: 0.851 AC: 1798 AN: 2112

Alfa AF: 0.810 Hom.: 2467

Bravo AF: 0.875

Asia WGS AF: 0.932 AC: 3243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.042
DANN	Benign	0.42
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs758294; hg19: chr17-32565120;