rs9586179

Variant names:

• chr13-103407737-T-C
• rs9586179

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 0.196 in 151,946 control chromosomes in the GnomAD database, including 7,958 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 0.20 (7958 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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: 0.196 AC: 29767 AN: 151828 Hom.: 7928 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.0718

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.196 AC: 29850 AN: 151946 Hom.: 7958 Cov.: 32 AF XY: 0.191 AC XY: 14186 AN XY: 74306

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.0461

Gnomad4 EAS AF: 0.0719

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.158

Alfa AF: 0.0522 Hom.: 1053

Bravo AF: 0.221

Asia WGS AF: 0.115 AC: 401 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9586179; hg19: chr13-104060087;