rs1327395

Variant names:

• chr9-25410996-C-A
• rs1327395

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0338 AC: 1404 AN: 41542

American (AMR) AF: 0.0896 AC: 1370 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1192 AN: 5156

South Asian (SAS) AF: 0.204 AC: 981 AN: 4818

European-Finnish (FIN) AF: 0.172 AC: 1812 AN: 10564

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10312 AN: 67994

Other (OTH) AF: 0.112 AC: 237 AN: 2110

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1327395; hg19: chr9-25410994;