rs4851823

Variant names:

• chr2-105644847-T-C
• rs4851823
• ENST00000720256.1:n.247T>C

Variant summary

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

The ENST00000720256.1(ENSG00000293966):​n.247T>C 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 0.22 in 152,104 control chromosomes in the GnomAD database, including 3,776 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 0.22 (3776 hom., cov: 32)
• Consequence: ENSG00000293966 ENST00000720256.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 2 publications found

Genes affected

ENSG00000293966 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720256.1. 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
	ENSG00000293966	ENST00000720256.1		n.247T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000293937	ENST00000720028.1		n.91-9127A>G		intron	N/A
	ENSG00000293937	ENST00000720029.1		n.260-9127A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33440 AN: 151986 Hom.: 3772 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.220 AC: 33454 AN: 152104 Hom.: 3776 Cov.: 32 AF XY: 0.220 AC XY: 16343 AN XY: 74326

African (AFR) AF: 0.265 AC: 10976 AN: 41480

American (AMR) AF: 0.230 AC: 3510 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1081 AN: 5150

South Asian (SAS) AF: 0.258 AC: 1241 AN: 4812

European-Finnish (FIN) AF: 0.140 AC: 1486 AN: 10582

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13388 AN: 68018

Other (OTH) AF: 0.239 AC: 506 AN: 2114

Alfa AF: 0.210 Hom.: 1839

Bravo AF: 0.229

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.99
DANN	Benign	0.30
PhyloP100		-0.76

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: rs4851823;

hg19: chr2-106261304;