rs2423191

Positions:

• chr20-7312888-C-A
• chr20-7312888-C-G
• chr20-7312888-C-T

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 0.407 in 151,894 control chromosomes in the GnomAD database, including 14,033 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 0.41 (14033 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

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 = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7312888C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61827 AN: 151776 Hom.: 14029 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.407 AC: 61836 AN: 151894 Hom.: 14033 Cov.: 32 AF XY: 0.411 AC XY: 30476 AN XY: 74230

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.396

Alfa AF: 0.449 Hom.: 7004

Bravo AF: 0.389

Asia WGS AF: 0.449 AC: 1560 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
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: rs2423191; hg19: chr20-7293535;