rs11143679

Variant names:

• chr9-73722598-C-T
• rs11143679
• ENST00000715873.1:n.166-3884C>T

Variant summary

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

The ENST00000715873.1(ENSG00000232590):​n.166-3884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,936 control chromosomes in the GnomAD database, including 15,302 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 0.41 (15302 hom., cov: 31)
• Consequence: ENSG00000232590 ENST00000715873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 3 publications found

Genes affected

ENSG00000232590 (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 (EAS) allele frequency at 95% confidence interval = 0.525 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
ENSG00000232590	ENST00000715873.1	n.166-3884C>T		intron_variant	Intron 3 of 3
ENSG00000293610	ENST00000715874.1	n.354+55480G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62556 AN: 151818 Hom.: 15303 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.412 AC: 62561 AN: 151936 Hom.: 15302 Cov.: 31 AF XY: 0.417 AC XY: 30913 AN XY: 74220

African (AFR) AF: 0.132 AC: 5481 AN: 41488

American (AMR) AF: 0.408 AC: 6225 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3470

East Asian (EAS) AF: 0.542 AC: 2772 AN: 5116

South Asian (SAS) AF: 0.527 AC: 2544 AN: 4824

European-Finnish (FIN) AF: 0.548 AC: 5787 AN: 10552

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35833 AN: 67932

Other (OTH) AF: 0.472 AC: 996 AN: 2110

Alfa AF: 0.433 Hom.: 2627

Bravo AF: 0.390

Asia WGS AF: 0.523 AC: 1813 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11143679; hg19: chr9-76337514;