rs1361314

Positions:

• chr9-8177862-A-C
• chr9-8177862-A-G

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 0.984 in 152,038 control chromosomes in the GnomAD database, including 73,662 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 0.98 (73662 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.987 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: 0.984 AC: 149530 AN: 151920 Hom.: 73613 Cov.: 30

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.986

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.982

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

GnomAD4 genome AF: 0.984 AC: 149638 AN: 152038 Hom.: 73662 Cov.: 30 AF XY: 0.985 AC XY: 73167 AN XY: 74298

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.986

Gnomad4 ASJ AF: 0.987

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.981

Alfa AF: 0.985 Hom.: 10493

Bravo AF: 0.981

Asia WGS AF: 0.965 AC: 3356 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1361314; hg19: chr9-8177862;