rs1475718

Variant names:

• chr9-134226324-G-A
• rs1475718
• ENST00000729187.1:n.254-602C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-134226324-G-A
• chr9-134226324-G-C

Variant summary

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

The ENST00000729187.1(ENSG00000295308):​n.254-602C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,044 control chromosomes in the GnomAD database, including 23,571 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 0.54 (23571 hom., cov: 32)
• Consequence: ENSG00000295308 ENST00000729187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793
• Publications: 7 publications found

Genes affected

ENSG00000295308 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729187.1. 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
	ENSG00000295308	ENST00000729187.1		n.254-602C>T		intron	N/A
	ENSG00000295308	ENST00000729186.1		n.-28C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82459 AN: 151926 Hom.: 23536 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.543 AC: 82537 AN: 152044 Hom.: 23571 Cov.: 32 AF XY: 0.540 AC XY: 40118 AN XY: 74316

African (AFR) AF: 0.717 AC: 29741 AN: 41484

American (AMR) AF: 0.542 AC: 8278 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2277 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1992 AN: 5160

South Asian (SAS) AF: 0.449 AC: 2167 AN: 4822

European-Finnish (FIN) AF: 0.489 AC: 5163 AN: 10562

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31021 AN: 67952

Other (OTH) AF: 0.543 AC: 1147 AN: 2114

Alfa AF: 0.500 Hom.: 7089

Bravo AF: 0.557

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs1475718; hg19: chr9-137118170; COSMIC: COSV60405051;