9-75657179-T-C

Variant names:

• chr9-75657179-T-C
• rs4745431

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.551

Alfa AF: 0.573 Hom.: 51126

Bravo AF: 0.560

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4745431; hg19: chr9-78272095;