9-8177453-G-C

Variant names:

• chr9-8177453-G-C
• rs1416585

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 0.327 in 151,954 control chromosomes in the GnomAD database, including 9,926 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 0.33 (9926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49732 AN: 151836 Hom.: 9931 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.0471

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.327 AC: 49715 AN: 151954 Hom.: 9926 Cov.: 32 AF XY: 0.330 AC XY: 24473 AN XY: 74240

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.0476

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.342

Alfa AF: 0.380 Hom.: 1519

Bravo AF: 0.304

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
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: rs1416585; hg19: chr9-8177453;