rs1328406

Variant names:

• chr9-79342883-C-T
• rs1328406

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 0.297 in 151,980 control chromosomes in the GnomAD database, including 6,826 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 0.30 (6826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462

ACMG classification

Verdict is Benign. Variant got -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 = 0.346 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: 0.297 AC: 45144 AN: 151862 Hom.: 6810 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.297 AC: 45176 AN: 151980 Hom.: 6826 Cov.: 32 AF XY: 0.300 AC XY: 22265 AN XY: 74274

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.290

Alfa AF: 0.281 Hom.: 5084

Bravo AF: 0.300

Asia WGS AF: 0.369 AC: 1286 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328406; hg19: chr9-81957798;