rs11143677

Variant names:

• chr9-73720400-G-A
• rs11143677
• ENST00000715873.1:n.166-6082G>A

Variant summary

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

The ENST00000715873.1(ENSG00000232590):​n.166-6082G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,962 control chromosomes in the GnomAD database, including 15,186 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 (15186 hom., cov: 33)
• Consequence: ENSG00000232590 ENST00000715873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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.166-6082G>A		intron_variant	Intron 3 of 3
ENSG00000293610	ENST00000715874.1	n.354+57678C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62282 AN: 151842 Hom.: 15186 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.410 AC: 62289 AN: 151962 Hom.: 15186 Cov.: 33 AF XY: 0.415 AC XY: 30788 AN XY: 74266

African (AFR) AF: 0.131 AC: 5457 AN: 41504

American (AMR) AF: 0.407 AC: 6200 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2238 AN: 3472

East Asian (EAS) AF: 0.541 AC: 2788 AN: 5156

South Asian (SAS) AF: 0.527 AC: 2534 AN: 4810

European-Finnish (FIN) AF: 0.547 AC: 5761 AN: 10538

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

European-Non Finnish (NFE) AF: 0.525 AC: 35656 AN: 67938

Other (OTH) AF: 0.469 AC: 986 AN: 2104

Alfa AF: 0.431 Hom.: 2603

Bravo AF: 0.388

Asia WGS AF: 0.521 AC: 1798 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.74
DANN	Benign	0.66
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11143677; hg19: chr9-76335316;