7-9036490-G-C

Variant names:

• chr7-9036490-G-C
• rs17158578

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 0.0311 in 152,024 control chromosomes in the GnomAD database, including 129 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 0.031 (129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0725 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0310 AC: 4708 AN: 151906 Hom.: 126 Cov.: 32

Gnomad AFR AF: 0.0743

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.0281

Gnomad FIN AF: 0.00386

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0311 AC: 4735 AN: 152024 Hom.: 129 Cov.: 32 AF XY: 0.0308 AC XY: 2291 AN XY: 74306

African (AFR) AF: 0.0747 AC: 3100 AN: 41498

American (AMR) AF: 0.0110 AC: 167 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3468

East Asian (EAS) AF: 0.0334 AC: 171 AN: 5126

South Asian (SAS) AF: 0.0280 AC: 135 AN: 4830

European-Finnish (FIN) AF: 0.00386 AC: 41 AN: 10614

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 896 AN: 67942

Other (OTH) AF: 0.0303 AC: 64 AN: 2112

Alfa AF: 0.00539 Hom.: 2

Bravo AF: 0.0333

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.93
DANN	Benign	0.39
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs17158578; hg19: chr7-9076120;