2-198757984-C-T

Variant names:

• chr2-198757984-C-T
• rs1533535
• ENST00000440609.1:n.98+14275G>A

Variant summary

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

The ENST00000440609.1(ENSG00000225421):​n.98+14275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,878 control chromosomes in the GnomAD database, including 24,872 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 0.56 (24872 hom., cov: 30)
• Consequence: ENSG00000225421 ENST00000440609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 4 publications found

Genes affected

ENSG00000225421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225421	ENST00000440609.1	TSL:4	n.98+14275G>A		intron	N/A
	ENSG00000225421	ENST00000748012.1		n.25+14275G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84849 AN: 151760 Hom.: 24852 Cov.: 30

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.559 AC: 84906 AN: 151878 Hom.: 24872 Cov.: 30 AF XY: 0.561 AC XY: 41660 AN XY: 74206

African (AFR) AF: 0.378 AC: 15660 AN: 41402

American (AMR) AF: 0.594 AC: 9062 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2056 AN: 3462

East Asian (EAS) AF: 0.432 AC: 2224 AN: 5144

South Asian (SAS) AF: 0.503 AC: 2421 AN: 4816

European-Finnish (FIN) AF: 0.716 AC: 7541 AN: 10534

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43950 AN: 67946

Other (OTH) AF: 0.562 AC: 1185 AN: 2108

Alfa AF: 0.622 Hom.: 13949

Bravo AF: 0.538

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1533535; hg19: chr2-199622708;