rs11190488

Variant names:

• chr10-100372246-C-T
• rs11190488
• ENST00000693438.3:n.1523G>A

Variant summary

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

The ENST00000693438.3(ENSG00000289301):​n.1523G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 151,928 control chromosomes in the GnomAD database, including 350 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 0.061 (350 hom., cov: 31)
• Consequence: ENSG00000289301 ENST00000693438.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489
• Publications: 3 publications found

Genes affected

ENSG00000289301 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289301	ENST00000693438.3	n.1523G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000289301	ENST00000769404.1	n.344-558G>A		intron_variant	Intron 1 of 1
ENSG00000289301	ENST00000769405.1	n.396-138G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 9260 AN: 151810 Hom.: 345 Cov.: 31

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0755

Gnomad OTH AF: 0.0596

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

GnomAD4 genome AF: 0.0611 AC: 9276 AN: 151928 Hom.: 350 Cov.: 31 AF XY: 0.0606 AC XY: 4501 AN XY: 74258

African (AFR) AF: 0.0474 AC: 1962 AN: 41420

American (AMR) AF: 0.0396 AC: 603 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3472

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.117 AC: 564 AN: 4802

European-Finnish (FIN) AF: 0.0454 AC: 479 AN: 10548

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0755 AC: 5130 AN: 67964

Other (OTH) AF: 0.0589 AC: 124 AN: 2104

Alfa AF: 0.0679 Hom.: 44

Bravo AF: 0.0585

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.6
DANN	Benign	0.65
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs11190488; hg19: chr10-102132003;