9-7274696-T-C

Variant names:

• chr9-7274696-T-C
• rs1887867

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 0.348 in 151,054 control chromosomes in the GnomAD database, including 9,861 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 0.35 (9861 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 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: 0.348 AC: 52464 AN: 150936 Hom.: 9854 Cov.: 29

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.348 AC: 52505 AN: 151054 Hom.: 9861 Cov.: 29 AF XY: 0.353 AC XY: 26026 AN XY: 73672

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.369

Alfa AF: 0.299 Hom.: 11887

Bravo AF: 0.354

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1887867; hg19: chr9-7274696;