rs4849125

Variant names:

• chr2-112819338-G-A
• rs4849125
• ENST00000670671.2:n.325C>T

Variant summary

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

The ENST00000670671.2(ENSG00000287937):​n.325C>T 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 0.577 in 151,384 control chromosomes in the GnomAD database, including 27,638 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 0.58 (27638 hom., cov: 27)
• Consequence: ENSG00000287937 ENST00000670671.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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.325C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000299339	ENST00000762712.1		n.345G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000299339	ENST00000762722.1		n.151G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87276 AN: 151266 Hom.: 27625 Cov.: 27

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.577 AC: 87308 AN: 151384 Hom.: 27638 Cov.: 27 AF XY: 0.581 AC XY: 42897 AN XY: 73896

African (AFR) AF: 0.295 AC: 12167 AN: 41252

American (AMR) AF: 0.636 AC: 9676 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2157 AN: 3464

East Asian (EAS) AF: 0.915 AC: 4651 AN: 5084

South Asian (SAS) AF: 0.604 AC: 2892 AN: 4790

European-Finnish (FIN) AF: 0.684 AC: 7148 AN: 10452

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46657 AN: 67824

Other (OTH) AF: 0.598 AC: 1256 AN: 2102

Alfa AF: 0.639 Hom.: 7610

Bravo AF: 0.566

Asia WGS AF: 0.700 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.096

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: rs4849125;

hg19: chr2-113576915;