9-78141452-T-C

Variant names:

• chr9-78141452-T-C
• rs6560625

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 0.449 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.448 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

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.421

Alfa AF: 0.253 Hom.: 1003

Bravo AF: 0.467

Asia WGS AF: 0.548 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6560625; hg19: chr9-80756368;