rs7836900

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000253322 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520426.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253322	ENST00000520426.1	TSL:4	n.273+71085C>T		intron	N/A

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

African (AFR) AF: 0.472 AC: 19526 AN: 41372

American (AMR) AF: 0.299 AC: 4557 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1063 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1858 AN: 5158

South Asian (SAS) AF: 0.452 AC: 2176 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5122 AN: 10490

Middle Eastern (MID) AF: 0.331 AC: 96 AN: 290

European-Non Finnish (NFE) AF: 0.385 AC: 26181 AN: 67966

Other (OTH) AF: 0.394 AC: 828 AN: 2102

Alfa AF: 0.398 Hom.: 2678

Bravo AF: 0.392

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.73
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7836900;

hg19: chr8-58628032;