rs13004902

Variant names:

• chr2-136270110-A-G
• rs13004902
• ENST00000837573.1:n.121-5412A>G

Variant summary

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

The ENST00000837573.1(ENSG00000308974):​n.121-5412A>G 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 152,160 control chromosomes in the GnomAD database, including 14,496 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 (14496 hom., cov: 32)
• Consequence: ENSG00000308974 ENST00000837573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837573.1. 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
	ENSG00000308974	ENST00000837573.1		n.121-5412A>G		intron	N/A
	ENSG00000308974	ENST00000837574.1		n.285-5412A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56154 AN: 152042 Hom.: 14500 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.369 AC: 56140 AN: 152160 Hom.: 14496 Cov.: 32 AF XY: 0.361 AC XY: 26878 AN XY: 74370

African (AFR) AF: 0.111 AC: 4596 AN: 41538

American (AMR) AF: 0.221 AC: 3380 AN: 15292

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

East Asian (EAS) AF: 0.0284 AC: 147 AN: 5184

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4826

European-Finnish (FIN) AF: 0.618 AC: 6528 AN: 10562

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

European-Non Finnish (NFE) AF: 0.568 AC: 38612 AN: 67970

Other (OTH) AF: 0.271 AC: 572 AN: 2112

Alfa AF: 0.447 Hom.: 2244

Bravo AF: 0.327

Asia WGS AF: 0.124 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.40
PhyloP100		-1.2

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: rs13004902;

hg19: chr2-137027680;