rs10987149

chr9-126095572-G-Achr9-126095572-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441473.1(ENSG00000232413):n.235+37758G>A variant causes a intron, non coding transcript 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: ENST00000441473.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000441473.1	n.235+37758G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.657

Alfa AF: 0.668 Hom.: 19841

Bravo AF: 0.618

Asia WGS AF: 0.736 AC: 2560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	11
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10987149; hg19: chr9-128857851;