9-75657179-T-C

Variant names:

• chr9-75657179-T-C
• rs4745431

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 0.558 in 152,102 control chromosomes in the GnomAD database, including 24,008 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 0.56 (24008 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 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: 0.558 AC: 84778 AN: 151986 Hom.: 23995 Cov.: 33

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.558 AC: 84819 AN: 152102 Hom.: 24008 Cov.: 33 AF XY: 0.562 AC XY: 41826 AN XY: 74364

African (AFR) AF: 0.470 AC: 19501 AN: 41466

American (AMR) AF: 0.630 AC: 9631 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1688 AN: 3472

East Asian (EAS) AF: 0.763 AC: 3950 AN: 5178

South Asian (SAS) AF: 0.597 AC: 2877 AN: 4818

European-Finnish (FIN) AF: 0.579 AC: 6128 AN: 10582

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39252 AN: 67978

Other (OTH) AF: 0.551 AC: 1165 AN: 2116

Alfa AF: 0.569 Hom.: 81859

Bravo AF: 0.560

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4745431; hg19: chr9-78272095;