9-4763176-T-C

Position:

• chr9-4763176-T-C

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 0.444 in 152,144 control chromosomes in the GnomAD database, including 16,184 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 0.44 (16184 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 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: 0.444 AC: 67431 AN: 152026 Hom.: 16176 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.444 AC: 67479 AN: 152144 Hom.: 16184 Cov.: 33 AF XY: 0.445 AC XY: 33102 AN XY: 74358

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.454

Alfa AF: 0.499 Hom.: 44094

Bravo AF: 0.432

Asia WGS AF: 0.614 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs385893; hg19: chr9-4763176;