rs10987149

Variant names:

• chr9-126095572-G-A
• rs10987149
• ENST00000441473.1:n.235+37758G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-126095572-G-A
• chr9-126095572-G-T

Variant summary

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

The ENST00000441473.1(ENSG00000232413):​n.235+37758G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,192 control chromosomes in the GnomAD database, including 31,699 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 0.64 (31699 hom., cov: 34)
• Consequence: ENSG00000232413 ENST00000441473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 1 publications found

Genes affected

ENSG00000232413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441473.1. 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
	ENSG00000232413	ENST00000441473.1	TSL:5	n.235+37758G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96780 AN: 152074 Hom.: 31695 Cov.: 34

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.721

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.636 AC: 96815 AN: 152192 Hom.: 31699 Cov.: 34 AF XY: 0.642 AC XY: 47765 AN XY: 74410

African (AFR) AF: 0.493 AC: 20476 AN: 41506

American (AMR) AF: 0.635 AC: 9715 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2627 AN: 3466

East Asian (EAS) AF: 0.805 AC: 4161 AN: 5168

South Asian (SAS) AF: 0.730 AC: 3526 AN: 4828

European-Finnish (FIN) AF: 0.743 AC: 7884 AN: 10610

Middle Eastern (MID) AF: 0.724 AC: 210 AN: 290

European-Non Finnish (NFE) AF: 0.678 AC: 46107 AN: 67994

Other (OTH) AF: 0.657 AC: 1390 AN: 2116

Alfa AF: 0.655 Hom.: 26414

Bravo AF: 0.618

Asia WGS AF: 0.736 AC: 2560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10987149;

hg19: chr9-128857851;