rs8007923

Positions:

• chr14-104190322-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 0.357 in 151,944 control chromosomes in the GnomAD database, including 11,351 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 0.36 (11351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66

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 (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54172 AN: 151826 Hom.: 11337 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.357 AC: 54210 AN: 151944 Hom.: 11351 Cov.: 32 AF XY: 0.357 AC XY: 26532 AN XY: 74226

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.362

Alfa AF: 0.440 Hom.: 23141

Bravo AF: 0.337

Asia WGS AF: 0.286 AC: 992 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	3.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8007923; hg19: chr14-104656659;