rs10501893

Variant names:

• chr11-98943620-C-T
• rs10501893
• ENST00000527345.1:n.38+1422G>A

Variant summary

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

The ENST00000527345.1(ENSG00000254830):​n.38+1422G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,876 control chromosomes in the GnomAD database, including 8,003 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 0.31 (8003 hom., cov: 32)
• Consequence: ENSG00000254830 ENST00000527345.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 2 publications found

Genes affected

ENSG00000254830 (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 (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527345.1. 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
	ENSG00000254830	ENST00000527345.1	TSL:3	n.38+1422G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46358 AN: 151758 Hom.: 7996 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.305 AC: 46376 AN: 151876 Hom.: 8003 Cov.: 32 AF XY: 0.309 AC XY: 22946 AN XY: 74202

African (AFR) AF: 0.151 AC: 6265 AN: 41486

American (AMR) AF: 0.436 AC: 6630 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3466

East Asian (EAS) AF: 0.362 AC: 1851 AN: 5112

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4824

European-Finnish (FIN) AF: 0.347 AC: 3662 AN: 10546

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23772 AN: 67910

Other (OTH) AF: 0.310 AC: 655 AN: 2112

Alfa AF: 0.342 Hom.: 12976

Bravo AF: 0.303

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.78
PhyloP100		-0.055

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: rs10501893;

hg19: chr11-98814350;