rs6819013

Positions:

• chr4-16906381-A-G

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 0.381 in 152,086 control chromosomes in the GnomAD database, including 12,432 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 0.38 (12432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 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: 0.381 AC: 57943 AN: 151968 Hom.: 12410 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.381 AC: 58013 AN: 152086 Hom.: 12432 Cov.: 32 AF XY: 0.377 AC XY: 28020 AN XY: 74334

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0756

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.351

Alfa AF: 0.333 Hom.: 5855

Bravo AF: 0.393

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.41
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6819013; hg19: chr4-16908004;