2-198658398-C-T

Variant names:

• chr2-198658398-C-T
• rs17229285
• ENST00000440609.1:n.99-78690G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000440609.1(ENSG00000225421):​n.99-78690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,736 control chromosomes in the GnomAD database, including 13,237 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 0.39 (13237 hom., cov: 32)
• Consequence: ENSG00000225421 ENST00000440609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.50
• Publications: 40 publications found

Genes affected

ENSG00000225421 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440609.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225421	ENST00000440609.1	TSL:4	n.99-78690G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58568 AN: 151618 Hom.: 13244 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.386 AC: 58575 AN: 151736 Hom.: 13237 Cov.: 32 AF XY: 0.386 AC XY: 28612 AN XY: 74166

African (AFR) AF: 0.145 AC: 6011 AN: 41420

American (AMR) AF: 0.416 AC: 6323 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3466

East Asian (EAS) AF: 0.283 AC: 1461 AN: 5166

South Asian (SAS) AF: 0.594 AC: 2862 AN: 4822

European-Finnish (FIN) AF: 0.443 AC: 4678 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33933 AN: 67812

Other (OTH) AF: 0.412 AC: 871 AN: 2112

Alfa AF: 0.459 Hom.: 41853

Bravo AF: 0.373

Asia WGS AF: 0.445 AC: 1544 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	18
DANN	Benign	0.77
PhyloP100		3.5

Splicing

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

Other links and lift over

dbSNP: rs17229285; hg19: chr2-199523122;