chr9-103582639-C-T

Variant names:

• chr9-103582639-C-T
• rs1396553

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 0.763 in 152,092 control chromosomes in the GnomAD database, including 44,499 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 0.76 (44499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 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: 0.762 AC: 115851 AN: 151974 Hom.: 44445 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.763 AC: 115972 AN: 152092 Hom.: 44499 Cov.: 32 AF XY: 0.766 AC XY: 56960 AN XY: 74336

African (AFR) AF: 0.797 AC: 33086 AN: 41490

American (AMR) AF: 0.818 AC: 12495 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2668 AN: 3470

East Asian (EAS) AF: 0.817 AC: 4210 AN: 5154

South Asian (SAS) AF: 0.658 AC: 3172 AN: 4820

European-Finnish (FIN) AF: 0.796 AC: 8416 AN: 10570

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49411 AN: 67990

Other (OTH) AF: 0.759 AC: 1599 AN: 2108

Alfa AF: 0.741 Hom.: 31530

Bravo AF: 0.772

Asia WGS AF: 0.749 AC: 2605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.2
DANN	Benign	0.52
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs1396553; hg19: chr9-106344921;