rs9298693

Variant names:

• chr9-13901410-G-A
• rs9298693
• XR_001746620.2:n.806-19420C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746620.2(LOC101929507):​n.806-19420C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,626 control chromosomes in the GnomAD database, including 18,453 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 0.47 (18453 hom., cov: 30)
• Consequence: LOC101929507 XR_001746620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

LOC101929507 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929507	XR_001746620.2	n.806-19420C>T		intron_variant	Intron 7 of 8
LOC101929507	XR_001746621.2	n.738-19420C>T		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71276 AN: 151508 Hom.: 18417 Cov.: 30

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.471 AC: 71373 AN: 151626 Hom.: 18453 Cov.: 30 AF XY: 0.458 AC XY: 33959 AN XY: 74116

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.494

Alfa AF: 0.458 Hom.: 2102

Bravo AF: 0.480

Asia WGS AF: 0.265 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9298693; hg19: chr9-13901409; COSMIC: COSV60333996;