rs7018475

Variant names:

• chr9-22137686-T-G
• rs7018475

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 0.274 in 152,018 control chromosomes in the GnomAD database, including 5,690 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 0.27 (5690 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 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: 0.274 AC: 41565 AN: 151898 Hom.: 5687 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.274 AC: 41577 AN: 152018 Hom.: 5690 Cov.: 31 AF XY: 0.275 AC XY: 20407 AN XY: 74308

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.297

Alfa AF: 0.274 Hom.: 10240

Bravo AF: 0.274

Asia WGS AF: 0.339 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7018475; hg19: chr9-22137685;