rs1342326

chr9-6190076-A-C

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 0.205 in 152,042 control chromosomes in the GnomAD database, including 3,818 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 0.21 (3818 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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 (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31102 AN: 151924 Hom.: 3800 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.205 AC: 31172 AN: 152042 Hom.: 3818 Cov.: 32 AF XY: 0.204 AC XY: 15167 AN XY: 74338

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.190

Alfa AF: 0.164 Hom.: 3688

Bravo AF: 0.212

Asia WGS AF: 0.0770 AC: 271 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	6.5
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342326; hg19: chr9-6190076;