11-92947847-C-T

Variant names:

• chr11-92947847-C-T
• rs10830956
• ENST00000532770.2:n.147-12378C>T

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.147-12378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,928 control chromosomes in the GnomAD database, including 8,441 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 0.33 (8441 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 23 publications found

Genes affected

ENSG00000254874 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532770.2. 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
	ENSG00000254874	ENST00000532770.2	TSL:2	n.147-12378C>T		intron	N/A
	ENSG00000254874	ENST00000749785.1		n.129-12378C>T		intron	N/A
	ENSG00000254874	ENST00000749786.1		n.116-12378C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49838 AN: 151808 Hom.: 8438 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.328 AC: 49882 AN: 151928 Hom.: 8441 Cov.: 32 AF XY: 0.330 AC XY: 24533 AN XY: 74254

African (AFR) AF: 0.395 AC: 16347 AN: 41392

American (AMR) AF: 0.240 AC: 3661 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3472

East Asian (EAS) AF: 0.446 AC: 2298 AN: 5150

South Asian (SAS) AF: 0.392 AC: 1883 AN: 4804

European-Finnish (FIN) AF: 0.355 AC: 3748 AN: 10552

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

European-Non Finnish (NFE) AF: 0.291 AC: 19798 AN: 67976

Other (OTH) AF: 0.314 AC: 664 AN: 2114

Alfa AF: 0.304 Hom.: 16260

Bravo AF: 0.321

Asia WGS AF: 0.358 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.24
PhyloP100		0.14

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: rs10830956;

hg19: chr11-92681013;