chr15-98229240-G-A

Variant names:

• chr15-98229240-G-A
• rs1442799
• ENST00000560360.2:n.313+28339C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000560360.2(ENSG00000259199):​n.313+28339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 152,218 control chromosomes in the GnomAD database, including 207 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 0.044 (207 hom., cov: 32)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08
• Publications: 0 publications found

Genes affected

ENSG00000259199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259199	ENST00000560360.2	n.313+28339C>T		intron_variant	Intron 3 of 4	5
ENSG00000259199	ENST00000717124.1	n.291+28339C>T		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.0444 AC: 6754 AN: 152100 Hom.: 207 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0266

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0446

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0444 AC: 6766 AN: 152218 Hom.: 207 Cov.: 32 AF XY: 0.0465 AC XY: 3464 AN XY: 74424

African (AFR) AF: 0.0292 AC: 1215 AN: 41546

American (AMR) AF: 0.0266 AC: 406 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0911 AC: 316 AN: 3470

East Asian (EAS) AF: 0.0523 AC: 271 AN: 5182

South Asian (SAS) AF: 0.113 AC: 543 AN: 4824

European-Finnish (FIN) AF: 0.0826 AC: 875 AN: 10588

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0446 AC: 3034 AN: 68008

Other (OTH) AF: 0.0455 AC: 96 AN: 2112

Alfa AF: 0.0443 Hom.: 26

Bravo AF: 0.0381

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	15
DANN	Benign	0.75
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs1442799; hg19: chr15-98772469;