rs4739199

Positions:

• chr8-21366663-C-T

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 0.505 in 151,956 control chromosomes in the GnomAD database, including 19,988 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 0.51 (19988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.505 AC: 76716 AN: 151840 Hom.: 19983 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.505 AC: 76748 AN: 151956 Hom.: 19988 Cov.: 32 AF XY: 0.496 AC XY: 36871 AN XY: 74266

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.498

Alfa AF: 0.523 Hom.: 27750

Bravo AF: 0.492

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4739199; hg19: chr8-21224174;