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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373831	XR_923759.3	n.72+59858C>T		intron_variant	Intron 1 of 3
LOC105373831	XR_923760.2	n.72+59858C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225421	ENST00000440609.1	n.98+59858C>T		intron_variant	Intron 1 of 2	4

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 v4.3

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

Other links and lift over

dbSNP: rs1518099; hg19: chr2-199577125;