2-112819325-A-G

Variant names:

• chr2-112819325-A-G
• rs4849124
• ENST00000670671.2:n.338T>C

Variant summary

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

The ENST00000670671.2(ENSG00000287937):​n.338T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,652 control chromosomes in the GnomAD database, including 27,884 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 0.57 (27884 hom., cov: 28)
• Consequence: ENSG00000287937 ENST00000670671.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 9 publications found

Genes affected

ENSG00000287937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670671.2. 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
	ENSG00000287937	ENST00000670671.2		n.338T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000299339	ENST00000762712.1		n.332A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000299339	ENST00000762722.1		n.138A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87068 AN: 151534 Hom.: 27872 Cov.: 28

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.574 AC: 87102 AN: 151652 Hom.: 27884 Cov.: 28 AF XY: 0.577 AC XY: 42736 AN XY: 74054

African (AFR) AF: 0.270 AC: 11188 AN: 41380

American (AMR) AF: 0.640 AC: 9745 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2157 AN: 3462

East Asian (EAS) AF: 0.916 AC: 4687 AN: 5116

South Asian (SAS) AF: 0.586 AC: 2822 AN: 4816

European-Finnish (FIN) AF: 0.686 AC: 7175 AN: 10464

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47376 AN: 67872

Other (OTH) AF: 0.593 AC: 1251 AN: 2108

Alfa AF: 0.653 Hom.: 107793

Bravo AF: 0.564

Asia WGS AF: 0.698 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.92
DANN	Benign	0.36
PhyloP100		-0.28

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: rs4849124;

hg19: chr2-113576902;