rs10147163

chr14-20361279-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 0.314 in 152,092 control chromosomes in the GnomAD database, including 7,945 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 (7945 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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: 0.314 AC: 47763 AN: 151974 Hom.: 7931 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.314 AC: 47821 AN: 152092 Hom.: 7945 Cov.: 33 AF XY: 0.313 AC XY: 23237 AN XY: 74344

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.286

Alfa AF: 0.312 Hom.: 961

Bravo AF: 0.312

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.9
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10147163; hg19: chr14-20829438;