rs4606813

Positions:

• chr18-76766320-G-A

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 0.494 in 152,076 control chromosomes in the GnomAD database, including 19,095 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 0.49 (19095 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 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: 0.494 AC: 75098 AN: 151958 Hom.: 19097 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.494 AC: 75122 AN: 152076 Hom.: 19095 Cov.: 33 AF XY: 0.493 AC XY: 36667 AN XY: 74326

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.493

Alfa AF: 0.544 Hom.: 46619

Bravo AF: 0.491

Asia WGS AF: 0.456 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4606813; hg19: chr18-74478276;