15-98234142-A-G

Variant names:

• chr15-98234142-A-G
• rs1442815
• ENST00000560360.2:n.313+23437T>C

Variant summary

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

The ENST00000560360.2(ENSG00000259199):​n.313+23437T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,160 control chromosomes in the GnomAD database, including 40,342 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 0.72 (40342 hom., cov: 33)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 3 publications found

Genes affected

ENSG00000259199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560360.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259199	ENST00000560360.2	TSL:5	n.313+23437T>C		intron	N/A
	ENSG00000259199	ENST00000717124.1		n.291+23437T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110142 AN: 152042 Hom.: 40290 Cov.: 33

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.725 AC: 110258 AN: 152160 Hom.: 40342 Cov.: 33 AF XY: 0.724 AC XY: 53836 AN XY: 74392

African (AFR) AF: 0.819 AC: 34024 AN: 41522

American (AMR) AF: 0.706 AC: 10800 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1950 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3252 AN: 5168

South Asian (SAS) AF: 0.655 AC: 3154 AN: 4814

European-Finnish (FIN) AF: 0.716 AC: 7577 AN: 10586

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47331 AN: 67994

Other (OTH) AF: 0.686 AC: 1449 AN: 2112

Alfa AF: 0.700 Hom.: 20663

Bravo AF: 0.726

Asia WGS AF: 0.641 AC: 2230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.091
DANN	Benign	0.55
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1442815; hg19: chr15-98777371;