2-198757984-C-T

Position:

• chr2-198757984-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000225421 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373831	XR_923759.3	n.72+14275G>A		intron_variant
LOC105373831	XR_923760.2	n.72+14275G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225421	ENST00000440609.1	n.98+14275G>A		intron_variant		4

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

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.562

Alfa AF: 0.618 Hom.: 7827

Bravo AF: 0.538

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1533535; hg19: chr2-199622708;