rs1836851

Variant names:

• chr8-31360966-G-A
• rs1836851
• ENST00000524022.1:n.214-23191G>A

Variant summary

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

The ENST00000524022.1(ENSG00000253377):​n.214-23191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,114 control chromosomes in the GnomAD database, including 11,886 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 0.38 (11886 hom., cov: 33)
• Consequence: ENSG00000253377 ENST00000524022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

Genes affected

ENSG00000253377 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929492	XR_949649.3	n.1019-28010G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253377	ENST00000524022.1	n.214-23191G>A		intron_variant	Intron 1 of 1	3
ENSG00000253377	ENST00000655813.1	n.268-23191G>A		intron_variant	Intron 1 of 1
ENSG00000253377	ENST00000670110.2	n.327-28010G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57292 AN: 151996 Hom.: 11861 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.377 AC: 57358 AN: 152114 Hom.: 11886 Cov.: 33 AF XY: 0.378 AC XY: 28066 AN XY: 74338

African (AFR) AF: 0.559 AC: 23189 AN: 41486

American (AMR) AF: 0.343 AC: 5242 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1089 AN: 5174

South Asian (SAS) AF: 0.268 AC: 1294 AN: 4832

European-Finnish (FIN) AF: 0.314 AC: 3315 AN: 10560

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20754 AN: 67988

Other (OTH) AF: 0.357 AC: 753 AN: 2108

Alfa AF: 0.331 Hom.: 16484

Bravo AF: 0.391

Asia WGS AF: 0.274 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.23
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1836851; hg19: chr8-31218482;