9-12397405-G-T

Variant names:

• chr9-12397405-G-T
• rs1360461

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 0.536 in 151,796 control chromosomes in the GnomAD database, including 23,008 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 0.54 (23008 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81303 AN: 151678 Hom.: 22991 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.536 AC: 81344 AN: 151796 Hom.: 23008 Cov.: 31 AF XY: 0.543 AC XY: 40251 AN XY: 74134

African (AFR) AF: 0.341 AC: 14112 AN: 41386

American (AMR) AF: 0.665 AC: 10138 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1491 AN: 3466

East Asian (EAS) AF: 0.708 AC: 3639 AN: 5140

South Asian (SAS) AF: 0.550 AC: 2648 AN: 4816

European-Finnish (FIN) AF: 0.680 AC: 7151 AN: 10514

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40316 AN: 67922

Other (OTH) AF: 0.538 AC: 1134 AN: 2108

Alfa AF: 0.570 Hom.: 69094

Bravo AF: 0.529

Asia WGS AF: 0.577 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.71
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1360461; hg19: chr9-12397405;