9-8118541-C-T

Position:

• chr9-8118541-C-T

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 0.452 in 151,792 control chromosomes in the GnomAD database, including 18,386 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 0.45 (18386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

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 (NFE) allele frequency at 95% confidence interval = 0.584 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: 0.452 AC: 68630 AN: 151674 Hom.: 18385 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.452 AC: 68630 AN: 151792 Hom.: 18386 Cov.: 32 AF XY: 0.459 AC XY: 34086 AN XY: 74214

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.470

Alfa AF: 0.495 Hom.: 3254

Bravo AF: 0.420

Asia WGS AF: 0.448 AC: 1556 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	2.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4742455; hg19: chr9-8118541; COSMIC: COSV69445961;