rs1327395

Positions:

• chr9-25410996-C-A
• chr9-25410996-C-T

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 0.118 in 152,148 control chromosomes in the GnomAD database, including 1,343 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 0.12 (1343 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 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: 0.118 AC: 17929 AN: 152032 Hom.: 1345 Cov.: 33

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.118 AC: 17925 AN: 152148 Hom.: 1343 Cov.: 33 AF XY: 0.121 AC XY: 8970 AN XY: 74368

Gnomad4 AFR AF: 0.0338

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0753 Hom.: 125

Bravo AF: 0.105

Asia WGS AF: 0.172 AC: 597 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1327395; hg19: chr9-25410994;