ENST00000776537.1:n.238+37G>A

Variant names:

• chr17-34251836-C-T
• rs3917878
• ENST00000776537.1:n.238+37G>A

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0996 in 152,236 control chromosomes in the GnomAD database, including 889 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 0.10 (889 hom., cov: 32)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 13 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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+37G>A		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.238+37G>A		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.236+37G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15136 AN: 152118 Hom.: 885 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0996 AC: 15156 AN: 152236 Hom.: 889 Cov.: 32 AF XY: 0.0981 AC XY: 7305 AN XY: 74430

African (AFR) AF: 0.161 AC: 6696 AN: 41518

American (AMR) AF: 0.0738 AC: 1128 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.102 AC: 491 AN: 4830

European-Finnish (FIN) AF: 0.0669 AC: 709 AN: 10604

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0824 AC: 5607 AN: 68026

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.0885 Hom.: 485

Bravo AF: 0.102

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs3917878; hg19: chr17-32578855;