rs1125441

Variant names:

• chr9-115752165-G-A
• rs1125441
• ENST00000832032.1:n.322-10603C>T

Variant summary

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

The ENST00000832032.1(ENSG00000228714):​n.322-10603C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,910 control chromosomes in the GnomAD database, including 1,557 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 0.13 (1557 hom., cov: 32)
• Consequence: ENSG00000228714 ENST00000832032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 3 publications found

Genes affected

ENSG00000228714 (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 = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376234	XR_930268.2	n.366+4439G>A		intron_variant	Intron 2 of 2
LOC105376234	XR_930269.2	n.366+4439G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228714	ENST00000832032.1	n.322-10603C>T		intron_variant	Intron 1 of 2
ENSG00000308189	ENST00000832372.1	n.305+4439G>A		intron_variant	Intron 2 of 3
ENSG00000308189	ENST00000832373.1	n.334+4439G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20017 AN: 151792 Hom.: 1551 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0714

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.132 AC: 20051 AN: 151910 Hom.: 1557 Cov.: 32 AF XY: 0.132 AC XY: 9766 AN XY: 74246

African (AFR) AF: 0.213 AC: 8833 AN: 41426

American (AMR) AF: 0.131 AC: 1990 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 248 AN: 3472

East Asian (EAS) AF: 0.0602 AC: 309 AN: 5132

South Asian (SAS) AF: 0.103 AC: 496 AN: 4818

European-Finnish (FIN) AF: 0.104 AC: 1097 AN: 10574

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0987 AC: 6707 AN: 67938

Other (OTH) AF: 0.124 AC: 263 AN: 2114

Alfa AF: 0.109 Hom.: 557

Bravo AF: 0.139

Asia WGS AF: 0.0910 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.39
DANN	Benign	0.33
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs1125441; hg19: chr9-118514444;