rs10968093

Variant names:

• chr9-27753229-G-A
• rs10968093
• ENST00000727209.1:n.116-603C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-27753229-G-A
• chr9-27753229-G-T

Variant summary

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

The ENST00000727209.1(ENSG00000294991):​n.116-603C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,158 control chromosomes in the GnomAD database, including 723 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 0.067 (723 hom., cov: 32)
• Consequence: ENSG00000294991 ENST00000727209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 4 publications found

Genes affected

ENSG00000294991 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902135	XM_047424284.1	c.188-8221G>A		intron_variant	Intron 2 of 2		XP_047280240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294991	ENST00000727209.1	n.116-603C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10113 AN: 152040 Hom.: 723 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0251

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0666 AC: 10131 AN: 152158 Hom.: 723 Cov.: 32 AF XY: 0.0671 AC XY: 4988 AN XY: 74382

African (AFR) AF: 0.171 AC: 7103 AN: 41498

American (AMR) AF: 0.0332 AC: 508 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.154 AC: 794 AN: 5168

South Asian (SAS) AF: 0.0251 AC: 121 AN: 4816

European-Finnish (FIN) AF: 0.0457 AC: 485 AN: 10608

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 897 AN: 68002

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

Alfa AF: 0.0277 Hom.: 839

Bravo AF: 0.0708

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.44
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10968093; hg19: chr9-27753227;