rs7035639

Positions:

• chr9-21189263-G-C

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 0.223 in 151,900 control chromosomes in the GnomAD database, including 4,213 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 0.22 (4213 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21189263G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33786 AN: 151782 Hom.: 4202 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.223 AC: 33850 AN: 151900 Hom.: 4213 Cov.: 32 AF XY: 0.223 AC XY: 16591 AN XY: 74240

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.215

Alfa AF: 0.206 Hom.: 419

Bravo AF: 0.233

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7035639; hg19: chr9-21189262;