rs10781135

Variant names:

• chr9-73290232-T-C
• rs10781135
• ENST00000715867.1:n.95-68576T>C

Variant summary

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

The ENST00000715867.1(ENSG00000293608):​n.95-68576T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,100 control chromosomes in the GnomAD database, including 7,566 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 0.28 (7566 hom., cov: 32)
• Consequence: ENSG00000293608 ENST00000715867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 7 publications found

Genes affected

ENSG00000293608 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927281	XR_001746723.2	n.67+30875T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293608	ENST00000715867.1	n.95-68576T>C		intron_variant	Intron 1 of 7
ENSG00000293608	ENST00000715868.1	n.100+30875T>C		intron_variant	Intron 1 of 7
ENSG00000293608	ENST00000715869.1	n.82+30875T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43202 AN: 151982 Hom.: 7566 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.284 AC: 43207 AN: 152100 Hom.: 7566 Cov.: 32 AF XY: 0.288 AC XY: 21387 AN XY: 74356

African (AFR) AF: 0.0782 AC: 3250 AN: 41540

American (AMR) AF: 0.270 AC: 4120 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1077 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2027 AN: 5160

South Asian (SAS) AF: 0.474 AC: 2286 AN: 4822

European-Finnish (FIN) AF: 0.352 AC: 3720 AN: 10554

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25741 AN: 67964

Other (OTH) AF: 0.304 AC: 641 AN: 2112

Alfa AF: 0.335 Hom.: 19237

Bravo AF: 0.266

Asia WGS AF: 0.380 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.41
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10781135; hg19: chr9-75905148;