rs10960291

Variant names:

• chr9-11827014-A-G
• rs10960291
• ENST00000649122.1:n.317+42355A>G

Variant summary

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

The ENST00000649122.1(ENSG00000285784):​n.317+42355A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,834 control chromosomes in the GnomAD database, including 3,448 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 0.19 (3448 hom., cov: 32)
• Consequence: ENSG00000285784 ENST00000649122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 2 publications found

Genes affected

ENSG00000285784 (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 (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929446	XR_242531.6	n.490-413T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285784	ENST00000649122.1	n.317+42355A>G		intron_variant	Intron 3 of 5
ENSG00000303032	ENST00000791318.1	n.458+2207T>C		intron_variant	Intron 2 of 2
ENSG00000303032	ENST00000791319.1	n.458+2207T>C		intron_variant	Intron 2 of 2
ENSG00000303032	ENST00000791320.1	n.500-413T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28688 AN: 151716 Hom.: 3449 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.189 AC: 28688 AN: 151834 Hom.: 3448 Cov.: 32 AF XY: 0.189 AC XY: 14006 AN XY: 74218

African (AFR) AF: 0.0444 AC: 1841 AN: 41498

American (AMR) AF: 0.177 AC: 2696 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 927 AN: 3460

East Asian (EAS) AF: 0.231 AC: 1186 AN: 5136

South Asian (SAS) AF: 0.179 AC: 862 AN: 4816

European-Finnish (FIN) AF: 0.241 AC: 2547 AN: 10580

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17912 AN: 67818

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.243 Hom.: 2497

Bravo AF: 0.178

Asia WGS AF: 0.205 AC: 712 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	3.9
DANN	Benign	0.73
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs10960291; hg19: chr9-11827014;