rs1843026

Variant names:

• chr8-76907621-G-A
• rs1843026
• ENST00000519660.1:n.88+2943G>A

Variant summary

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

The ENST00000519660.1(ENSG00000253416):​n.88+2943G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,914 control chromosomes in the GnomAD database, including 21,214 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 0.51 (21214 hom., cov: 31)
• Consequence: ENSG00000253416 ENST00000519660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 3 publications found

Genes affected

ENSG00000253416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519660.1. 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
	ENSG00000253416	ENST00000519660.1	TSL:3	n.88+2943G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77133 AN: 151796 Hom.: 21216 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.508 AC: 77170 AN: 151914 Hom.: 21214 Cov.: 31 AF XY: 0.507 AC XY: 37629 AN XY: 74238

African (AFR) AF: 0.291 AC: 12044 AN: 41418

American (AMR) AF: 0.558 AC: 8509 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2098 AN: 3468

East Asian (EAS) AF: 0.438 AC: 2260 AN: 5154

South Asian (SAS) AF: 0.516 AC: 2485 AN: 4818

European-Finnish (FIN) AF: 0.598 AC: 6312 AN: 10558

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.612 AC: 41578 AN: 67932

Other (OTH) AF: 0.542 AC: 1144 AN: 2112

Alfa AF: 0.544 Hom.: 3839

Bravo AF: 0.495

Asia WGS AF: 0.456 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.78
PhyloP100		-1.6

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: rs1843026;

hg19: chr8-77819857;