rs6819013

Variant names:

• chr4-16906381-A-G
• rs6819013

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 0.381 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.578 AC: 23978 AN: 41460

American (AMR) AF: 0.346 AC: 5291 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3468

East Asian (EAS) AF: 0.0756 AC: 391 AN: 5174

South Asian (SAS) AF: 0.206 AC: 991 AN: 4818

European-Finnish (FIN) AF: 0.337 AC: 3559 AN: 10570

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21883 AN: 67990

Other (OTH) AF: 0.351 AC: 742 AN: 2112

Alfa AF: 0.341 Hom.: 21577

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs6819013; hg19: chr4-16908004;