rs12691881

Variant names:

• chr2-136272098-A-G
• rs12691881
• ENST00000837573.1:n.121-3424A>G

Variant summary

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

The ENST00000837573.1(ENSG00000308974):​n.121-3424A>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 152,096 control chromosomes in the GnomAD database, including 14,497 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 (14497 hom., cov: 32)
• Consequence: ENSG00000308974 ENST00000837573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 6 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=-0.83).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308974	ENST00000837573.1		n.121-3424A>G		intron	N/A
	ENSG00000308974	ENST00000837574.1		n.285-3424A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56141 AN: 151978 Hom.: 14501 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.619

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: 56127 AN: 152096 Hom.: 14497 Cov.: 32 AF XY: 0.361 AC XY: 26876 AN XY: 74364

African (AFR) AF: 0.110 AC: 4590 AN: 41540

American (AMR) AF: 0.221 AC: 3383 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 602 AN: 3468

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5184

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4820

European-Finnish (FIN) AF: 0.619 AC: 6530 AN: 10550

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

European-Non Finnish (NFE) AF: 0.568 AC: 38609 AN: 67946

Other (OTH) AF: 0.271 AC: 573 AN: 2112

Alfa AF: 0.460 Hom.: 4828

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	-0.83
CADD	Benign	5.8
DANN	Benign	0.84
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12691881; hg19: chr2-137029668;