rs1543239

Variant names:

• chr7-69208109-G-A
• rs1543239
• ENST00000670444.1:n.531-20796C>T

Variant summary

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

The ENST00000670444.1(ENSG00000225718):​n.531-20796C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,192 control chromosomes in the GnomAD database, including 2,617 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 0.18 (2617 hom., cov: 33)
• Consequence: ENSG00000225718 ENST00000670444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 4 publications found

Genes affected

ENSG00000225718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670444.1. 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
	ENSG00000225718	ENST00000670444.1		n.531-20796C>T		intron	N/A
	ENSG00000225718	ENST00000716162.1		n.628+4599C>T		intron	N/A
	ENSG00000225718	ENST00000829733.1		n.198+16487C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27526 AN: 152074 Hom.: 2613 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.181 AC: 27555 AN: 152192 Hom.: 2617 Cov.: 33 AF XY: 0.182 AC XY: 13564 AN XY: 74408

African (AFR) AF: 0.195 AC: 8113 AN: 41532

American (AMR) AF: 0.181 AC: 2760 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3470

East Asian (EAS) AF: 0.177 AC: 918 AN: 5176

South Asian (SAS) AF: 0.310 AC: 1492 AN: 4818

European-Finnish (FIN) AF: 0.102 AC: 1077 AN: 10594

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11664 AN: 67996

Other (OTH) AF: 0.202 AC: 428 AN: 2116

Alfa AF: 0.180 Hom.: 11006

Bravo AF: 0.185

Asia WGS AF: 0.243 AC: 846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.52
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1543239; hg19: chr7-68673096;