rs10895516

Variant names:

• chr11-103737242-G-A
• rs10895516
• ENST00000533459.1:n.128-32344C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-103737242-G-A
• chr11-103737242-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533459.1(ENSG00000254987):​n.128-32344C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 152,166 control chromosomes in the GnomAD database, including 134 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 0.027 (134 hom., cov: 32)
• Consequence: ENSG00000254987 ENST00000533459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

Genes affected

ENSG00000254987 (HGNC:56909):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 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
ENSG00000254987	ENST00000533459.1	n.128-32344C>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4139 AN: 152048 Hom.: 134 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.00972

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0272 AC: 4140 AN: 152166 Hom.: 134 Cov.: 32 AF XY: 0.0280 AC XY: 2084 AN XY: 74360

Gnomad4 AFR AF: 0.0372

Gnomad4 AMR AF: 0.0181

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.00972

Gnomad4 NFE AF: 0.0146

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0179 Hom.: 64

Bravo AF: 0.0280

Asia WGS AF: 0.0960 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10895516; hg19: chr11-103607970;