rs7029145

Variant names:

• chr9-27882655-C-T
• rs7029145

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 0.359 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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

African (AFR) AF: 0.136 AC: 5659 AN: 41460

American (AMR) AF: 0.396 AC: 6044 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2251 AN: 5156

South Asian (SAS) AF: 0.395 AC: 1903 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4566 AN: 10530

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31065 AN: 67952

Other (OTH) AF: 0.387 AC: 818 AN: 2112

Alfa AF: 0.423 Hom.: 32590

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
PhyloP100		0.33

Splicing

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

Other links and lift over

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