rs731824

Variant names:

• chr1-230887325-C-A
• rs731824
• ENST00000654598.1:n.241+2172G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-230887325-C-A
• chr1-230887325-C-T

Variant summary

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

The ENST00000654598.1(ENSG00000288037):​n.241+2172G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,916 control chromosomes in the GnomAD database, including 25,613 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 0.58 (25613 hom., cov: 32)
• Consequence: ENSG00000288037 ENST00000654598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 3 publications found

Genes affected

ENSG00000288037 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904547	XR_007066938.1	n.885+2172G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288037	ENST00000654598.1	n.241+2172G>T		intron_variant	Intron 2 of 2
ENSG00000288037	ENST00000836702.1	n.288+2172G>T		intron_variant	Intron 2 of 2
ENSG00000288037	ENST00000836703.1	n.346+2172G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87571 AN: 151800 Hom.: 25601 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.577 AC: 87598 AN: 151916 Hom.: 25613 Cov.: 32 AF XY: 0.572 AC XY: 42482 AN XY: 74254

African (AFR) AF: 0.500 AC: 20691 AN: 41410

American (AMR) AF: 0.547 AC: 8363 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2532 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2359 AN: 5132

South Asian (SAS) AF: 0.676 AC: 3252 AN: 4812

European-Finnish (FIN) AF: 0.522 AC: 5495 AN: 10522

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42759 AN: 67968

Other (OTH) AF: 0.624 AC: 1319 AN: 2114

Alfa AF: 0.565 Hom.: 11585

Bravo AF: 0.571

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.57
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs731824; hg19: chr1-231023071;