rs7014900

Positions:

• chr8-114566078-T-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 0.28 in 151,894 control chromosomes in the GnomAD database, including 6,751 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 0.28 (6751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42386 AN: 151778 Hom.: 6733 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.280 AC: 42457 AN: 151894 Hom.: 6751 Cov.: 32 AF XY: 0.279 AC XY: 20735 AN XY: 74246

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.265

Alfa AF: 0.222 Hom.: 8301

Bravo AF: 0.295

Asia WGS AF: 0.317 AC: 1101 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7014900; hg19: chr8-115578307;