9-7274696-T-C

Variant names:

• chr9-7274696-T-C
• rs1887867

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 0.348 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.348 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

African (AFR) AF: 0.379 AC: 15593 AN: 41090

American (AMR) AF: 0.359 AC: 5417 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 991 AN: 3466

East Asian (EAS) AF: 0.784 AC: 4011 AN: 5118

South Asian (SAS) AF: 0.430 AC: 2042 AN: 4752

European-Finnish (FIN) AF: 0.345 AC: 3591 AN: 10402

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19719 AN: 67846

Other (OTH) AF: 0.369 AC: 770 AN: 2086

Alfa AF: 0.314 Hom.: 31922

Bravo AF: 0.354

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1887867; hg19: chr9-7274696;