9-4976186-C-T

Variant names:

• chr9-4976186-C-T
• rs10124001

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 0.0444 in 152,176 control chromosomes in the GnomAD database, including 235 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 0.044 (235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0924 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: 0.0442 AC: 6726 AN: 152058 Hom.: 235 Cov.: 32

Gnomad AFR AF: 0.0870

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0176

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0444 AC: 6751 AN: 152176 Hom.: 235 Cov.: 32 AF XY: 0.0450 AC XY: 3344 AN XY: 74382

African (AFR) AF: 0.0874 AC: 3624 AN: 41484

American (AMR) AF: 0.0256 AC: 391 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3472

East Asian (EAS) AF: 0.0995 AC: 516 AN: 5188

South Asian (SAS) AF: 0.0674 AC: 325 AN: 4820

European-Finnish (FIN) AF: 0.0532 AC: 564 AN: 10596

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0176 AC: 1200 AN: 68014

Other (OTH) AF: 0.0327 AC: 69 AN: 2108

Alfa AF: 0.0184 Hom.: 18

Bravo AF: 0.0429

Asia WGS AF: 0.0950 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.59
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs10124001; hg19: chr9-4976186;