2-236684247-C-T

Variant names:

• chr2-236684247-C-T
• rs2254387
• ENST00000779927.1:n.368C>T

Variant summary

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

The ENST00000779927.1(ENSG00000301575):​n.368C>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 0.0654 in 152,228 control chromosomes in the GnomAD database, including 397 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 0.065 (397 hom., cov: 32)
• Consequence: ENSG00000301575 ENST00000779927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 1 publications found

Genes affected

ENSG00000301575 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779927.1. 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
	ENSG00000301575	ENST00000779927.1		n.368C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000301575	ENST00000779928.1		n.179C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000301575	ENST00000779929.1		n.295C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0654 AC: 9948 AN: 152110 Hom.: 397 Cov.: 32

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00290

Gnomad SAS AF: 0.0276

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0654 AC: 9950 AN: 152228 Hom.: 397 Cov.: 32 AF XY: 0.0672 AC XY: 5001 AN XY: 74428

African (AFR) AF: 0.0514 AC: 2135 AN: 41540

American (AMR) AF: 0.0428 AC: 655 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3470

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5168

South Asian (SAS) AF: 0.0280 AC: 135 AN: 4820

European-Finnish (FIN) AF: 0.138 AC: 1461 AN: 10602

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4994 AN: 68018

Other (OTH) AF: 0.0549 AC: 116 AN: 2112

Alfa AF: 0.0745 Hom.: 55

Bravo AF: 0.0583

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.83
PhyloP100		-0.072

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: rs2254387;

hg19: chr2-237592890;