rs4620729

chr11-69212868-C-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 0.52 in 152,088 control chromosomes in the GnomAD database, including 21,916 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 0.52 (21916 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

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 = 0.667 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: 0.519 AC: 78943 AN: 151970 Hom.: 21872 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.520 AC: 79039 AN: 152088 Hom.: 21916 Cov.: 33 AF XY: 0.512 AC XY: 38030 AN XY: 74346

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.0655

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.534

Alfa AF: 0.527 Hom.: 5495

Bravo AF: 0.524

Asia WGS AF: 0.297 AC: 1032 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	1.5
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4620729; hg19: chr11-68980335;