chr9-8177862-A-C

Variant names:

• chr9-8177862-A-C
• rs1361314

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.984 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

African (AFR) AF: 0.971 AC: 40294 AN: 41482

American (AMR) AF: 0.986 AC: 15023 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3425 AN: 3470

East Asian (EAS) AF: 0.937 AC: 4834 AN: 5160

South Asian (SAS) AF: 0.994 AC: 4774 AN: 4802

European-Finnish (FIN) AF: 0.998 AC: 10594 AN: 10610

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67503 AN: 67958

Other (OTH) AF: 0.981 AC: 2073 AN: 2114

Alfa AF: 0.984 Hom.: 10850

Bravo AF: 0.981

Asia WGS AF: 0.965 AC: 3356 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.46
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1361314; hg19: chr9-8177862;