rs7632070

Positions:

• chr3-117308665-A-G

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 0.38 in 152,090 control chromosomes in the GnomAD database, including 13,023 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 0.38 (13023 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117308665A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57855 AN: 151970 Hom.: 13023 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.380 AC: 57848 AN: 152090 Hom.: 13023 Cov.: 32 AF XY: 0.380 AC XY: 28287 AN XY: 74344

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.396

Alfa AF: 0.459 Hom.: 3501

Bravo AF: 0.366

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7632070; hg19: chr3-117027512;