9-8118541-C-T

Variant names:

• chr9-8118541-C-T
• rs4742455

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;