rs2981099

Positions:

• chr8-72943292-G-A
• chr8-72943292-G-C
• chr8-72943292-G-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 0.288 in 151,972 control chromosomes in the GnomAD database, including 7,897 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 0.29 (7897 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

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 (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.72943292G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43735 AN: 151854 Hom.: 7888 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.288 AC: 43783 AN: 151972 Hom.: 7897 Cov.: 33 AF XY: 0.296 AC XY: 21985 AN XY: 74266

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.298

Alfa AF: 0.248 Hom.: 1297

Bravo AF: 0.303

Asia WGS AF: 0.602 AC: 2085 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2981099; hg19: chr8-73855527;