rs163818

Positions:

• chr5-14071948-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 0.478 in 151,828 control chromosomes in the GnomAD database, including 20,690 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 0.48 (20690 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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 = 0.793 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: 0.478 AC: 72447 AN: 151710 Hom.: 20634 Cov.: 30

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.478 AC: 72577 AN: 151828 Hom.: 20690 Cov.: 30 AF XY: 0.474 AC XY: 35165 AN XY: 74182

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.0979

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.440

Alfa AF: 0.393 Hom.: 12648

Bravo AF: 0.485

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs163818; hg19: chr5-14072057;