rs1202524

Variant names:

• chr1-230815426-G-A
• rs1202524
• ENST00000717079.1:n.400+9238C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-230815426-G-A
• chr1-230815426-G-C
• chr1-230815426-G-T

Variant summary

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

The ENST00000717079.1(ENSG00000225656):​n.400+9238C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,182 control chromosomes in the GnomAD database, including 46,575 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 0.78 (46575 hom., cov: 32)
• Consequence: ENSG00000225656 ENST00000717079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 11 publications found

Genes affected

ENSG00000225656 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717079.1. 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
	ENSG00000225656	ENST00000717079.1		n.400+9238C>T		intron	N/A
	ENSG00000225656	ENST00000789895.1		n.121+9238C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117929 AN: 152064 Hom.: 46526 Cov.: 32

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.776 AC: 118037 AN: 152182 Hom.: 46575 Cov.: 32 AF XY: 0.780 AC XY: 58003 AN XY: 74402

African (AFR) AF: 0.921 AC: 38231 AN: 41532

American (AMR) AF: 0.745 AC: 11398 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3470

East Asian (EAS) AF: 0.885 AC: 4588 AN: 5182

South Asian (SAS) AF: 0.912 AC: 4394 AN: 4818

European-Finnish (FIN) AF: 0.708 AC: 7492 AN: 10578

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46863 AN: 67986

Other (OTH) AF: 0.763 AC: 1613 AN: 2114

Alfa AF: 0.724 Hom.: 67876

Bravo AF: 0.781

Asia WGS AF: 0.899 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.30
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1202524; hg19: chr1-230951172;