rs2080161

Positions:

• chr7-13291525-A-C
• chr7-13291525-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 0.196 in 149,920 control chromosomes in the GnomAD database, including 3,836 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 0.20 (3836 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.13291525A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000411542.1	n.237-18684A>C		intron_variant		4
ENSG00000229618	ENST00000638964.1	n.609-18684A>C		intron_variant		5
ENSG00000229618	ENST00000639998.1	n.608-18684A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29409 AN: 149824 Hom.: 3823 Cov.: 30

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.196 AC: 29441 AN: 149920 Hom.: 3836 Cov.: 30 AF XY: 0.204 AC XY: 14916 AN XY: 73126

Gnomad4 AFR AF: 0.0669

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.202

Alfa AF: 0.207 Hom.: 4245

Bravo AF: 0.205

Asia WGS AF: 0.243 AC: 839 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.37
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2080161; hg19: chr7-13331150;