rs163818

Variant names:

• chr5-14071948-T-C
• rs163818

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.800 AC: 33130 AN: 41398

American (AMR) AF: 0.338 AC: 5162 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1373 AN: 3460

East Asian (EAS) AF: 0.0979 AC: 506 AN: 5168

South Asian (SAS) AF: 0.340 AC: 1635 AN: 4806

European-Finnish (FIN) AF: 0.389 AC: 4089 AN: 10506

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.374 AC: 25432 AN: 67930

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.437 Hom.: 25574

Bravo AF: 0.485

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs163818; hg19: chr5-14072057;