9-4763176-T-C

Variant names:

• chr9-4763176-T-C
• rs385893

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 0.444 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
• Publications: 54 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.274 AC: 11363 AN: 41504

American (AMR) AF: 0.449 AC: 6859 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1418 AN: 3472

East Asian (EAS) AF: 0.790 AC: 4095 AN: 5184

South Asian (SAS) AF: 0.504 AC: 2426 AN: 4816

European-Finnish (FIN) AF: 0.482 AC: 5096 AN: 10566

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34819 AN: 68000

Other (OTH) AF: 0.454 AC: 956 AN: 2108

Alfa AF: 0.493 Hom.: 90548

Bravo AF: 0.432

Asia WGS AF: 0.614 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.67
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs385893; hg19: chr9-4763176;