7-45926196-A-G

Variant names:

• chr7-45926196-A-G
• rs2453836
• ENST00000833715.1:n.186+869A>G

Variant summary

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

The ENST00000833715.1(ENSG00000308377):​n.186+869A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,820 control chromosomes in the GnomAD database, including 2,788 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 0.19 (2788 hom., cov: 32)
• Consequence: ENSG00000308377 ENST00000833715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891
• Publications: 15 publications found

Genes affected

ENSG00000308377 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 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
ENSG00000308377	ENST00000833715.1	n.186+869A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28353 AN: 151700 Hom.: 2782 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0317

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.187 AC: 28388 AN: 151820 Hom.: 2788 Cov.: 32 AF XY: 0.185 AC XY: 13734 AN XY: 74178

African (AFR) AF: 0.207 AC: 8550 AN: 41346

American (AMR) AF: 0.172 AC: 2629 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3468

East Asian (EAS) AF: 0.0318 AC: 165 AN: 5186

South Asian (SAS) AF: 0.288 AC: 1385 AN: 4806

European-Finnish (FIN) AF: 0.125 AC: 1315 AN: 10534

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12797 AN: 67924

Other (OTH) AF: 0.227 AC: 477 AN: 2104

Alfa AF: 0.190 Hom.: 12411

Bravo AF: 0.188

Asia WGS AF: 0.197 AC: 684 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs2453836; hg19: chr7-45965795;