rs10502195

Variant names:

• chr11-114833570-T-C
• rs10502195
• ENST00000751459.1:n.192+39111A>G

Variant summary

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

The ENST00000751459.1(ENSG00000297869):​n.192+39111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,932 control chromosomes in the GnomAD database, including 9,131 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 0.34 (9131 hom., cov: 32)
• Consequence: ENSG00000297869 ENST00000751459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 1 publications found

Genes affected

ENSG00000297869 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369506	XR_948042.3	n.86+39111A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297869	ENST00000751459.1	n.192+39111A>G		intron_variant	Intron 2 of 3
ENSG00000297869	ENST00000751460.1	n.214+39111A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51702 AN: 151814 Hom.: 9123 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.340 AC: 51732 AN: 151932 Hom.: 9131 Cov.: 32 AF XY: 0.347 AC XY: 25787 AN XY: 74256

African (AFR) AF: 0.342 AC: 14149 AN: 41402

American (AMR) AF: 0.406 AC: 6203 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1154 AN: 3472

East Asian (EAS) AF: 0.573 AC: 2948 AN: 5146

South Asian (SAS) AF: 0.417 AC: 2007 AN: 4818

European-Finnish (FIN) AF: 0.304 AC: 3208 AN: 10564

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20994 AN: 67942

Other (OTH) AF: 0.320 AC: 674 AN: 2108

Alfa AF: 0.322 Hom.: 1637

Bravo AF: 0.343

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.85
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs10502195; hg19: chr11-114704292;