2-210737692-T-C

Variant names:

• chr2-210737692-T-C
• rs16844874
• ENST00000737540.1:n.435+2093T>C

Variant summary

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

The ENST00000737540.1(ENSG00000296241):​n.435+2093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,222 control chromosomes in the GnomAD database, including 2,286 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 0.16 (2286 hom., cov: 32)
• Consequence: ENSG00000296241 ENST00000737540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 5 publications found

Genes affected

ENSG00000296241 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737540.1. 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
	ENSG00000296241	ENST00000737540.1		n.435+2093T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24148 AN: 152104 Hom.: 2282 Cov.: 32

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.159 AC: 24153 AN: 152222 Hom.: 2286 Cov.: 32 AF XY: 0.166 AC XY: 12347 AN XY: 74430

African (AFR) AF: 0.0597 AC: 2480 AN: 41558

American (AMR) AF: 0.202 AC: 3082 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3468

East Asian (EAS) AF: 0.153 AC: 790 AN: 5172

South Asian (SAS) AF: 0.188 AC: 908 AN: 4824

European-Finnish (FIN) AF: 0.319 AC: 3371 AN: 10572

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12436 AN: 68020

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.169 Hom.: 438

Bravo AF: 0.146

Asia WGS AF: 0.159 AC: 556 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		1.5

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: rs16844874;

hg19: chr2-211602416;