rs1840054

Variant names:

• chr11-97384512-C-A
• rs1840054
• ENST00000742725.1:n.131+21330C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-97384512-C-A
• chr11-97384512-C-G
• chr11-97384512-C-T

Variant summary

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

The ENST00000742725.1(ENSG00000296812):​n.131+21330C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,906 control chromosomes in the GnomAD database, including 17,085 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 0.43 (17085 hom., cov: 32)
• Consequence: ENSG00000296812 ENST00000742725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 4 publications found

Genes affected

ENSG00000296812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742725.1. 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
	ENSG00000296812	ENST00000742725.1		n.131+21330C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66029 AN: 151792 Hom.: 17091 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.435 AC: 66030 AN: 151906 Hom.: 17085 Cov.: 32 AF XY: 0.440 AC XY: 32665 AN XY: 74248

African (AFR) AF: 0.142 AC: 5906 AN: 41464

American (AMR) AF: 0.508 AC: 7750 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2056 AN: 3466

East Asian (EAS) AF: 0.823 AC: 4242 AN: 5152

South Asian (SAS) AF: 0.536 AC: 2583 AN: 4820

European-Finnish (FIN) AF: 0.539 AC: 5677 AN: 10540

Middle Eastern (MID) AF: 0.600 AC: 174 AN: 290

European-Non Finnish (NFE) AF: 0.533 AC: 36211 AN: 67912

Other (OTH) AF: 0.484 AC: 1018 AN: 2104

Alfa AF: 0.521 Hom.: 32777

Bravo AF: 0.424

Asia WGS AF: 0.633 AC: 2198 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.055
DANN	Benign	0.82
PhyloP100		-1.7

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: rs1840054;

hg19: chr11-97255512;