rs184891496

Positions:

• chr9-38750582-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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 0.017 (38 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0174 (1988/113970) while in subpopulation AFR AF= 0.0416 (1201/28862). AF 95% confidence interval is 0.0397. There are 38 homozygotes in gnomad4. There are 943 alleles in male gnomad4 subpopulation. Median coverage is 19. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 38 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0174 AC: 1987 AN: 113976 Hom.: 39 Cov.: 19

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.00256

Gnomad AMR AF: 0.00779

Gnomad ASJ AF: 0.00959

Gnomad EAS AF: 0.00146

Gnomad SAS AF: 0.00525

Gnomad FIN AF: 0.00861

Gnomad MID AF: 0.00424

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.00680

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

GnomAD4 genome AF: 0.0174 AC: 1988 AN: 113970 Hom.: 38 Cov.: 19 AF XY: 0.0171 AC XY: 943 AN XY: 55180

Gnomad4 AFR AF: 0.0416

Gnomad4 AMR AF: 0.00779

Gnomad4 ASJ AF: 0.00959

Gnomad4 EAS AF: 0.00147

Gnomad4 SAS AF: 0.00527

Gnomad4 FIN AF: 0.00861

Gnomad4 NFE AF: 0.0107

Gnomad4 OTH AF: 0.00737

Alfa AF: 0.126 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs184891496; hg19: chr9-38750579;