rs13018756

Variant names:

• chr2-136250665-C-T
• rs13018756
• ENST00000837573.1:n.120+4140C>T

Variant summary

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

The ENST00000837573.1(ENSG00000308974):​n.120+4140C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,032 control chromosomes in the GnomAD database, including 14,491 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 0.37 (14491 hom., cov: 32)
• Consequence: ENSG00000308974 ENST00000837573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 4 publications found

Genes affected

ENSG00000308974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308974	ENST00000837573.1	n.120+4140C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56146 AN: 151914 Hom.: 14495 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.369 AC: 56133 AN: 152032 Hom.: 14491 Cov.: 32 AF XY: 0.362 AC XY: 26871 AN XY: 74302

African (AFR) AF: 0.111 AC: 4608 AN: 41484

American (AMR) AF: 0.222 AC: 3387 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3470

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5178

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4816

European-Finnish (FIN) AF: 0.618 AC: 6514 AN: 10532

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38613 AN: 67958

Other (OTH) AF: 0.270 AC: 568 AN: 2104

Alfa AF: 0.460 Hom.: 5214

Bravo AF: 0.327

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.34
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs13018756; hg19: chr2-137008235;