11-32342641-G-A

Variant names:

• chr11-32342641-G-A
• rs2057178
• ENST00000525689.2:n.122+647C>T

Variant summary

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

The ENST00000525689.2(ENSG00000293378):​n.122+647C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,356 control chromosomes in the GnomAD database, including 2,852 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 0.18 (2852 hom., cov: 31)
• Consequence: ENSG00000293378 ENST00000525689.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 49 publications found

Genes affected

ENSG00000293378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525689.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293378	ENST00000525689.2	TSL:3	n.122+647C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27213 AN: 151288 Hom.: 2844 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0586

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.180 AC: 27228 AN: 151356 Hom.: 2852 Cov.: 31 AF XY: 0.175 AC XY: 12921 AN XY: 73818

African (AFR) AF: 0.289 AC: 11928 AN: 41224

American (AMR) AF: 0.113 AC: 1720 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.0581 AC: 299 AN: 5144

South Asian (SAS) AF: 0.222 AC: 1057 AN: 4766

European-Finnish (FIN) AF: 0.0698 AC: 719 AN: 10306

Middle Eastern (MID) AF: 0.203 AC: 58 AN: 286

European-Non Finnish (NFE) AF: 0.152 AC: 10320 AN: 67942

Other (OTH) AF: 0.173 AC: 361 AN: 2086

Alfa AF: 0.160 Hom.: 6532

Bravo AF: 0.182

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.68
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2057178; hg19: chr11-32364187;