2-198763183-T-C

Variant names:

• chr2-198763183-T-C
• rs10202112
• ENST00000440609.1:n.98+9076A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.735 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

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
	ENSG00000225421	ENST00000440609.1	TSL:4	n.98+9076A>G		intron	N/A
	ENSG00000225421	ENST00000748012.1		n.25+9076A>G		intron	N/A

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

African (AFR) AF: 0.619 AC: 25647 AN: 41444

American (AMR) AF: 0.678 AC: 10357 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2343 AN: 3466

East Asian (EAS) AF: 0.454 AC: 2335 AN: 5148

South Asian (SAS) AF: 0.526 AC: 2528 AN: 4810

European-Finnish (FIN) AF: 0.761 AC: 8041 AN: 10568

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50369 AN: 67988

Other (OTH) AF: 0.668 AC: 1412 AN: 2114

Alfa AF: 0.714 Hom.: 163323

Bravo AF: 0.671

Asia WGS AF: 0.506 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.84

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: rs10202112;

hg19: chr2-199627907;