rs7003899

Positions:

• chr8-139596073-T-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 0.308 in 151,406 control chromosomes in the GnomAD database, including 7,384 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 0.31 (7384 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

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 (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.139596073T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46559 AN: 151286 Hom.: 7378 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.308 AC: 46588 AN: 151406 Hom.: 7384 Cov.: 33 AF XY: 0.306 AC XY: 22670 AN XY: 74012

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.333

Alfa AF: 0.312 Hom.: 9975

Bravo AF: 0.297

Asia WGS AF: 0.363 AC: 1263 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	3.6
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: rs7003899; hg19: chr8-140608316;