2-198763183-T-C

Position:

• chr2-198763183-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440609.1(ENSG00000225421):​n.98+9076A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,014 control chromosomes in the GnomAD database, including 36,039 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 0.68 (36039 hom., cov: 32)
• Consequence: ENSG00000225421 ENST00000440609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845

Genes affected

ENSG00000225421 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373831	XR_923759.3	n.72+9076A>G		intron_variant
LOC105373831	XR_923760.2	n.72+9076A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225421	ENST00000440609.1	n.98+9076A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103922 AN: 151896 Hom.: 36017 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.684 AC: 103997 AN: 152014 Hom.: 36039 Cov.: 32 AF XY: 0.681 AC XY: 50602 AN XY: 74272

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.668

Alfa AF: 0.717 Hom.: 78613

Bravo AF: 0.671

Asia WGS AF: 0.506 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10202112; hg19: chr2-199627907;