rs7836900

Variant names:

• chr8-57715473-G-A
• rs7836900
• ENST00000520426.1:n.273+71085C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520426.1(ENSG00000253322):​n.273+71085C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,812 control chromosomes in the GnomAD database, including 12,998 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 0.41 (12998 hom., cov: 31)
• Consequence: ENSG00000253322 ENST00000520426.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

ENSG00000253322 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 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
ENSG00000253322	ENST00000520426.1	n.273+71085C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61727 AN: 151696 Hom.: 12970 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.407 AC: 61810 AN: 151812 Hom.: 12998 Cov.: 31 AF XY: 0.411 AC XY: 30454 AN XY: 74186

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.394

Alfa AF: 0.396 Hom.: 2587

Bravo AF: 0.392

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7836900; hg19: chr8-58628032;