rs1317294

Positions:

• chr9-14697024-G-A

Variant summary

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

The variant allele was found at a frequency of 0.242 in 151,986 control chromosomes in the GnomAD database, including 4,993 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 0.24 (4993 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.747

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36753 AN: 151868 Hom.: 4966 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.242 AC: 36844 AN: 151986 Hom.: 4993 Cov.: 31 AF XY: 0.243 AC XY: 18023 AN XY: 74282

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.271

Alfa AF: 0.203 Hom.: 1336

Bravo AF: 0.254

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317294; hg19: chr9-14697022;