9-5350548-C-T

Variant names:

• chr9-5350548-C-T
• rs4742085

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 0.478 in 152,050 control chromosomes in the GnomAD database, including 18,748 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 0.48 (18748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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: 0.477 AC: 72502 AN: 151930 Hom.: 18711 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.478 AC: 72612 AN: 152050 Hom.: 18748 Cov.: 32 AF XY: 0.476 AC XY: 35383 AN XY: 74332

African (AFR) AF: 0.673 AC: 27924 AN: 41470

American (AMR) AF: 0.467 AC: 7125 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2249 AN: 5178

South Asian (SAS) AF: 0.545 AC: 2623 AN: 4816

European-Finnish (FIN) AF: 0.348 AC: 3679 AN: 10582

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25816 AN: 67950

Other (OTH) AF: 0.458 AC: 964 AN: 2106

Alfa AF: 0.416 Hom.: 2307

Bravo AF: 0.495

Asia WGS AF: 0.512 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.6
DANN	Benign	0.58
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4742085; hg19: chr9-5350548; COSMIC: COSV74188448;