rs7077836

Variant names:

• chr10-130953235-G-A
• rs7077836
• ENST00000769416.1:n.495-14925G>A

Variant summary

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

The ENST00000769416.1(ENSG00000300141):​n.495-14925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,188 control chromosomes in the GnomAD database, including 1,980 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 0.15 (1980 hom., cov: 33)
• Consequence: ENSG00000300141 ENST00000769416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 9 publications found

Genes affected

ENSG00000300141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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
ENSG00000300141	ENST00000769416.1	n.495-14925G>A		intron_variant	Intron 3 of 3
ENSG00000300141	ENST00000769417.1	n.446-8310G>A		intron_variant	Intron 3 of 4
ENSG00000300141	ENST00000769418.1	n.869-8310G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23029 AN: 152070 Hom.: 1983 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.151 AC: 23036 AN: 152188 Hom.: 1980 Cov.: 33 AF XY: 0.153 AC XY: 11404 AN XY: 74404

African (AFR) AF: 0.125 AC: 5190 AN: 41536

American (AMR) AF: 0.123 AC: 1876 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2016 AN: 5142

South Asian (SAS) AF: 0.152 AC: 733 AN: 4828

European-Finnish (FIN) AF: 0.197 AC: 2087 AN: 10594

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10195 AN: 68006

Other (OTH) AF: 0.143 AC: 301 AN: 2110

Alfa AF: 0.139 Hom.: 236

Bravo AF: 0.146

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7077836; hg19: chr10-132751498;