rs2417531

Variant names:

• chr9-104500901-G-A
• rs2417531
• ENST00000745188.1:n.506+29296C>T

Variant summary

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

The ENST00000745188.1(ENSG00000297079):​n.506+29296C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,994 control chromosomes in the GnomAD database, including 3,356 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 0.19 (3356 hom., cov: 30)
• Consequence: ENSG00000297079 ENST00000745188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 0 publications found

Genes affected

ENSG00000297079 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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
ENSG00000297079	ENST00000745188.1	n.506+29296C>T		intron_variant	Intron 3 of 8
ENSG00000297079	ENST00000745189.1	n.534-29913C>T		intron_variant	Intron 3 of 4
ENSG00000297079	ENST00000745190.1	n.556-285C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28135 AN: 151876 Hom.: 3353 Cov.: 30

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.185 AC: 28175 AN: 151994 Hom.: 3356 Cov.: 30 AF XY: 0.185 AC XY: 13738 AN XY: 74284

African (AFR) AF: 0.322 AC: 13348 AN: 41418

American (AMR) AF: 0.157 AC: 2398 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1783 AN: 5164

South Asian (SAS) AF: 0.174 AC: 836 AN: 4816

European-Finnish (FIN) AF: 0.102 AC: 1074 AN: 10554

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7504 AN: 67988

Other (OTH) AF: 0.190 AC: 400 AN: 2110

Alfa AF: 0.143 Hom.: 6827

Bravo AF: 0.198

Asia WGS AF: 0.282 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.24
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2417531; hg19: chr9-107263182;