2-240859849-C-T

Variant names:

• chr2-240859849-C-T
• rs4538195
• ENST00000750632.1:n.321G>A

Variant summary

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

The ENST00000750632.1(ENSG00000297735):​n.321G>A 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 0.0386 in 152,246 control chromosomes in the GnomAD database, including 154 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 0.039 (154 hom., cov: 32)
• Consequence: ENSG00000297735 ENST00000750632.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 2 publications found

Genes affected

ENSG00000297735 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750632.1. 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
	ENSG00000297735	ENST00000750632.1		n.321G>A		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000297735	ENST00000750633.1		n.312G>A		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000297735	ENST00000750635.1		n.279G>A		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5875 AN: 152128 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0386 AC: 5873 AN: 152246 Hom.: 154 Cov.: 32 AF XY: 0.0375 AC XY: 2795 AN XY: 74438

African (AFR) AF: 0.0108 AC: 448 AN: 41548

American (AMR) AF: 0.0347 AC: 530 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4820

European-Finnish (FIN) AF: 0.0637 AC: 675 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0586 AC: 3986 AN: 68020

Other (OTH) AF: 0.0379 AC: 80 AN: 2112

Alfa AF: 0.0452 Hom.: 85

Bravo AF: 0.0360

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.75
PhyloP100		0.21

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: rs4538195;

hg19: chr2-241799266;