rs875643

Variant names:

• chr22-23891811-G-A
• rs875643
• ENST00000433835.3:c.432-2961G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-23891811-G-A
• chr22-23891811-G-T

Variant summary

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

The ENST00000433835.3(ENSG00000251357):​c.432-2961G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,130 control chromosomes in the GnomAD database, including 15,308 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 0.44 (15308 hom., cov: 33)
• Consequence: ENSG00000251357 ENST00000433835.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 24 publications found

Genes affected

ENSG00000251357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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
ENSG00000251357	ENST00000433835.3	c.432-2961G>A		intron_variant	Intron 4 of 5	5		ENSP00000400325.3
ENSG00000290199	ENST00000717616.1	n.213-345C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67413 AN: 152012 Hom.: 15285 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.444 AC: 67488 AN: 152130 Hom.: 15308 Cov.: 33 AF XY: 0.441 AC XY: 32825 AN XY: 74364

African (AFR) AF: 0.543 AC: 22546 AN: 41508

American (AMR) AF: 0.386 AC: 5902 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3472

East Asian (EAS) AF: 0.287 AC: 1485 AN: 5174

South Asian (SAS) AF: 0.454 AC: 2185 AN: 4818

European-Finnish (FIN) AF: 0.399 AC: 4216 AN: 10570

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28182 AN: 67986

Other (OTH) AF: 0.436 AC: 918 AN: 2104

Alfa AF: 0.427 Hom.: 44907

Bravo AF: 0.448

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.71
PhyloP100		-1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs875643; hg19: chr22-24233998;