rs2755238

Variant names:

• chr13-40536133-T-C
• rs2755238
• ENST00000636651.2:n.1459+23376A>G

Variant summary

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

The ENST00000636651.2(ENSG00000288542):​n.1459+23376A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.079 in 152,246 control chromosomes in the GnomAD database, including 568 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 0.079 (568 hom., cov: 32)
• Consequence: ENSG00000288542 ENST00000636651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 8 publications found

Genes affected

ENSG00000288542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636651.2. 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
	ENSG00000288542	ENST00000636651.2	TSL:5	n.1459+23376A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 12024 AN: 152128 Hom.: 567 Cov.: 32

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.0790 AC: 12026 AN: 152246 Hom.: 568 Cov.: 32 AF XY: 0.0754 AC XY: 5611 AN XY: 74436

African (AFR) AF: 0.0466 AC: 1937 AN: 41538

American (AMR) AF: 0.0980 AC: 1499 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0416 AC: 201 AN: 4826

European-Finnish (FIN) AF: 0.0702 AC: 744 AN: 10592

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0997 AC: 6778 AN: 68012

Other (OTH) AF: 0.120 AC: 254 AN: 2114

Alfa AF: 0.0892 Hom.: 170

Bravo AF: 0.0803

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.10
DANN	Benign	0.46
PhyloP100		-1.3

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: rs2755238;

hg19: chr13-41110270;