11-95714875-C-T

Variant names:

• chr11-95714875-C-T
• rs10501830
• ENST00000648353.1:n.526-29844C>T

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.526-29844C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,008 control chromosomes in the GnomAD database, including 1,978 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 0.11 (1978 hom., cov: 32)
• Consequence: ENSG00000285842 ENST00000648353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 1 publications found

Genes affected

ENSG00000285842 (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 (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648353.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285842	ENST00000648353.1		n.526-29844C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16112 AN: 151888 Hom.: 1964 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0839

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

GnomAD4 genome AF: 0.106 AC: 16159 AN: 152008 Hom.: 1978 Cov.: 32 AF XY: 0.106 AC XY: 7867 AN XY: 74308

African (AFR) AF: 0.291 AC: 12031 AN: 41394

American (AMR) AF: 0.125 AC: 1915 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3464

East Asian (EAS) AF: 0.111 AC: 573 AN: 5168

South Asian (SAS) AF: 0.0811 AC: 390 AN: 4810

European-Finnish (FIN) AF: 0.0245 AC: 259 AN: 10588

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0109 AC: 739 AN: 68000

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0610 Hom.: 133

Bravo AF: 0.124

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.73
PhyloP100		0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10501830;

hg19: chr11-95448039;