rs7029145

Variant names:

• chr9-27882655-C-T
• rs7029145

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 0.359 in 151,952 control chromosomes in the GnomAD database, including 11,454 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 0.36 (11454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.360 AC: 54592 AN: 151834 Hom.: 11453 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.359 AC: 54606 AN: 151952 Hom.: 11454 Cov.: 32 AF XY: 0.360 AC XY: 26707 AN XY: 74270

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.387

Alfa AF: 0.444 Hom.: 24571

Bravo AF: 0.349

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7029145; hg19: chr9-27882653; COSMIC: COSV69455649;