chr2-212742038-T-C

Variant names:

• chr2-212742038-T-C
• rs16849204
• ENST00000415387.1:n.381+150647A>G

Variant summary

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

The ENST00000415387.1(ENSG00000273118):​n.381+150647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 152,294 control chromosomes in the GnomAD database, including 354 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 0.060 (354 hom., cov: 31)
• Consequence: ENSG00000273118 ENST00000415387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897
• Publications: 0 publications found

Genes affected

ENSG00000273118 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415387.1. 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
	ENSG00000273118	ENST00000415387.1	TSL:3	n.381+150647A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9106 AN: 152176 Hom.: 353 Cov.: 31

Gnomad AFR AF: 0.0262

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.0725

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0598 AC: 9111 AN: 152294 Hom.: 354 Cov.: 31 AF XY: 0.0607 AC XY: 4520 AN XY: 74462

African (AFR) AF: 0.0261 AC: 1087 AN: 41576

American (AMR) AF: 0.0579 AC: 885 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.211 AC: 1093 AN: 5184

South Asian (SAS) AF: 0.0867 AC: 418 AN: 4822

European-Finnish (FIN) AF: 0.0725 AC: 769 AN: 10608

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0671 AC: 4563 AN: 68020

Other (OTH) AF: 0.0516 AC: 109 AN: 2112

Alfa AF: 0.0573 Hom.: 173

Bravo AF: 0.0579

Asia WGS AF: 0.111 AC: 385 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		0.90
Mutation Taster		=100/0	polymorphism

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: rs16849204;

hg19: chr2-213606762;