2-105644323-C-T

Variant names:

• chr2-105644323-C-T
• rs4851821
• ENST00000720031.1:n.49G>A

Variant summary

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

The ENST00000720031.1(ENSG00000293937):​n.49G>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 0.365 in 151,934 control chromosomes in the GnomAD database, including 10,135 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 0.36 (10135 hom., cov: 32)
• Consequence: ENSG00000293937 ENST00000720031.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 4 publications found

Genes affected

ENSG00000293937 (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 (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720031.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293937	ENST00000720031.1		n.49G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000293937	ENST00000720028.1		n.91-8603G>A		intron	N/A
	ENSG00000293937	ENST00000720029.1		n.260-8603G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55402 AN: 151816 Hom.: 10133 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.365 AC: 55422 AN: 151934 Hom.: 10135 Cov.: 32 AF XY: 0.363 AC XY: 26972 AN XY: 74278

African (AFR) AF: 0.378 AC: 15666 AN: 41402

American (AMR) AF: 0.337 AC: 5149 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1282 AN: 5160

South Asian (SAS) AF: 0.391 AC: 1883 AN: 4814

European-Finnish (FIN) AF: 0.305 AC: 3225 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25203 AN: 67944

Other (OTH) AF: 0.379 AC: 797 AN: 2104

Alfa AF: 0.368 Hom.: 17780

Bravo AF: 0.362

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4851821; hg19: chr2-106260780;