chr4-154530035-A-G

Variant names:

• chr4-154530035-A-G
• rs6819508

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 0.808 in 151,980 control chromosomes in the GnomAD database, including 50,291 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 0.81 (50291 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 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: 0.808 AC: 122665 AN: 151862 Hom.: 50271 Cov.: 30

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.808 AC: 122736 AN: 151980 Hom.: 50291 Cov.: 30 AF XY: 0.809 AC XY: 60071 AN XY: 74288

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.839

Alfa AF: 0.855 Hom.: 50233

Bravo AF: 0.803

Asia WGS AF: 0.907 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6819508; hg19: chr4-155451187;