rs17242130

Variant names:

• chr5-81859087-A-C
• rs17242130
• ENST00000781317.1:n.297+21536A>C

Variant summary

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

The ENST00000781317.1(ENSG00000287938):​n.297+21536A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 151,512 control chromosomes in the GnomAD database, including 559 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 0.079 (559 hom., cov: 31)
• Consequence: ENSG00000287938 ENST00000781317.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• Publications: 3 publications found

Genes affected

ENSG00000287938 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000781317.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287938	ENST00000781317.1		n.297+21536A>C		intron	N/A
	ENSG00000287938	ENST00000781318.1		n.271+21536A>C		intron	N/A
	ENSG00000287938	ENST00000781319.1		n.152+5830A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12036 AN: 151410 Hom.: 560 Cov.: 31

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.0795 AC: 12042 AN: 151512 Hom.: 559 Cov.: 31 AF XY: 0.0765 AC XY: 5658 AN XY: 73988

African (AFR) AF: 0.0506 AC: 2087 AN: 41272

American (AMR) AF: 0.0730 AC: 1110 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0842 AC: 292 AN: 3466

East Asian (EAS) AF: 0.000776 AC: 4 AN: 5152

South Asian (SAS) AF: 0.0464 AC: 222 AN: 4780

European-Finnish (FIN) AF: 0.0694 AC: 722 AN: 10408

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7342 AN: 67914

Other (OTH) AF: 0.0883 AC: 186 AN: 2106

Alfa AF: 0.0961 Hom.: 1575

Bravo AF: 0.0795

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.68
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs17242130; hg19: chr5-81154906;