2-120323893-G-T

Variant names:

• chr2-120323893-G-T
• rs934721
• ENST00000437837.1:n.133-1630G>T

Variant summary

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

The ENST00000437837.1(ENSG00000235840):​n.133-1630G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,146 control chromosomes in the GnomAD database, including 53,906 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 0.84 (53906 hom., cov: 32)
• Consequence: ENSG00000235840 ENST00000437837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 4 publications found

Genes affected

ENSG00000235840 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437837.1. 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
	ENSG00000235840	ENST00000437837.1	TSL:4	n.133-1630G>T		intron	N/A
	ENSG00000235840	ENST00000725912.1		n.227-3957G>T		intron	N/A
	ENSG00000235840	ENST00000725913.1		n.196-1630G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127195 AN: 152028 Hom.: 53854 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.837 AC: 127300 AN: 152146 Hom.: 53906 Cov.: 32 AF XY: 0.830 AC XY: 61728 AN XY: 74378

African (AFR) AF: 0.763 AC: 31667 AN: 41492

American (AMR) AF: 0.853 AC: 13053 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3003 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2500 AN: 5142

South Asian (SAS) AF: 0.731 AC: 3521 AN: 4814

European-Finnish (FIN) AF: 0.850 AC: 9012 AN: 10598

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.908 AC: 61740 AN: 68010

Other (OTH) AF: 0.841 AC: 1780 AN: 2116

Alfa AF: 0.887 Hom.: 99704

Bravo AF: 0.832

Asia WGS AF: 0.610 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.33
DANN	Benign	0.58
PhyloP100		-2.5

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: rs934721;

hg19: chr2-121081469;