9-78141452-T-C

Variant names:

• chr9-78141452-T-C
• rs6560625

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 0.449 in 151,712 control chromosomes in the GnomAD database, including 19,705 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 0.45 (19705 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67970 AN: 151598 Hom.: 19649 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.449 AC: 68094 AN: 151712 Hom.: 19705 Cov.: 31 AF XY: 0.451 AC XY: 33444 AN XY: 74110

African (AFR) AF: 0.823 AC: 33967 AN: 41294

American (AMR) AF: 0.361 AC: 5505 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 959 AN: 3464

East Asian (EAS) AF: 0.569 AC: 2923 AN: 5134

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4816

European-Finnish (FIN) AF: 0.360 AC: 3771 AN: 10482

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17510 AN: 67944

Other (OTH) AF: 0.421 AC: 886 AN: 2104

Alfa AF: 0.274 Hom.: 1246

Bravo AF: 0.467

Asia WGS AF: 0.548 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6560625; hg19: chr9-80756368;