rs17423970

Variant names:

• chr15-48009867-G-A
• rs17423970
• ENST00000560900.1:n.258+17096G>A

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.258+17096G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,108 control chromosomes in the GnomAD database, including 9,162 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 0.30 (9162 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 2 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560900.1. 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
	ENSG00000259754	ENST00000560900.1	TSL:4	n.258+17096G>A		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.251+17096G>A		intron	N/A
	ENSG00000259754	ENST00000665188.1		n.220+11712G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46374 AN: 151990 Hom.: 9163 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.305 AC: 46364 AN: 152108 Hom.: 9162 Cov.: 32 AF XY: 0.306 AC XY: 22755 AN XY: 74354

African (AFR) AF: 0.0885 AC: 3674 AN: 41532

American (AMR) AF: 0.245 AC: 3738 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1348 AN: 3468

East Asian (EAS) AF: 0.0239 AC: 124 AN: 5184

South Asian (SAS) AF: 0.320 AC: 1541 AN: 4816

European-Finnish (FIN) AF: 0.501 AC: 5288 AN: 10556

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29551 AN: 67958

Other (OTH) AF: 0.292 AC: 618 AN: 2116

Alfa AF: 0.375 Hom.: 15191

Bravo AF: 0.272

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.64
PhyloP100		1.8

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: rs17423970;

hg19: chr15-48302064;