9-36314569-C-T

Variant names:

• chr9-36314569-C-T
• rs17385743
• XR_001746660.2:n.2578-2148C>T

Variant summary

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

The XR_001746660.2(LOC102724322):​n.2578-2148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,032 control chromosomes in the GnomAD database, including 1,815 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 0.14 (1815 hom., cov: 31)
• Consequence: LOC102724322 XR_001746660.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 2 publications found

Genes affected

LOC102724322 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20688 AN: 151914 Hom.: 1814 Cov.: 31

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.136 AC: 20687 AN: 152032 Hom.: 1815 Cov.: 31 AF XY: 0.140 AC XY: 10372 AN XY: 74306

African (AFR) AF: 0.0360 AC: 1492 AN: 41498

American (AMR) AF: 0.183 AC: 2792 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3470

East Asian (EAS) AF: 0.0892 AC: 461 AN: 5168

South Asian (SAS) AF: 0.117 AC: 565 AN: 4812

European-Finnish (FIN) AF: 0.226 AC: 2380 AN: 10542

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12126 AN: 67978

Other (OTH) AF: 0.147 AC: 310 AN: 2106

Alfa AF: 0.155 Hom.: 1677

Bravo AF: 0.131

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.75
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs17385743; hg19: chr9-36314566; COSMIC: COSV69460488;