9-75693141-C-T

Variant names:

• chr9-75693141-C-T
• rs4745437

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 0.571 in 151,918 control chromosomes in the GnomAD database, including 25,707 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 0.57 (25707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 4 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 = 0.963 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86643 AN: 151800 Hom.: 25682 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.571 AC: 86720 AN: 151918 Hom.: 25707 Cov.: 32 AF XY: 0.576 AC XY: 42780 AN XY: 74248

African (AFR) AF: 0.470 AC: 19454 AN: 41412

American (AMR) AF: 0.693 AC: 10581 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1760 AN: 3468

East Asian (EAS) AF: 0.986 AC: 5089 AN: 5162

South Asian (SAS) AF: 0.759 AC: 3654 AN: 4816

European-Finnish (FIN) AF: 0.501 AC: 5281 AN: 10534

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38909 AN: 67936

Other (OTH) AF: 0.602 AC: 1271 AN: 2112

Alfa AF: 0.583 Hom.: 44307

Bravo AF: 0.582

Asia WGS AF: 0.863 AC: 3002 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	1.7
DANN	Benign	0.22
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4745437; hg19: chr9-78308057;