rs1518099

Variant names:

• chr2-198712401-G-A
• rs1518099
• ENST00000440609.1:n.98+59858C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-198712401-G-A
• chr2-198712401-G-T

Variant summary

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

The ENST00000440609.1(ENSG00000225421):​n.98+59858C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,004 control chromosomes in the GnomAD database, including 37,868 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 0.70 (37868 hom., cov: 31)
• Consequence: ENSG00000225421 ENST00000440609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 7 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=-0.99).
• 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+59858C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106175 AN: 151886 Hom.: 37835 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.699 AC: 106263 AN: 152004 Hom.: 37868 Cov.: 31 AF XY: 0.699 AC XY: 51923 AN XY: 74270

African (AFR) AF: 0.664 AC: 27489 AN: 41428

American (AMR) AF: 0.710 AC: 10830 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2526 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2149 AN: 5156

South Asian (SAS) AF: 0.407 AC: 1956 AN: 4804

European-Finnish (FIN) AF: 0.820 AC: 8680 AN: 10580

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50357 AN: 67990

Other (OTH) AF: 0.706 AC: 1490 AN: 2110

Alfa AF: 0.716 Hom.: 64514

Bravo AF: 0.689

Asia WGS AF: 0.440 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.014
DANN	Benign	0.59
PhyloP100		-3.0

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: rs1518099;

hg19: chr2-199577125;