rs4612756

Positions:

• chr11-93624988-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 0.596 in 151,824 control chromosomes in the GnomAD database, including 27,334 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 0.60 (27334 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.596 AC: 90389 AN: 151706 Hom.: 27304 Cov.: 30

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.596 AC: 90470 AN: 151824 Hom.: 27334 Cov.: 30 AF XY: 0.596 AC XY: 44227 AN XY: 74182

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.596

Alfa AF: 0.586 Hom.: 11378

Bravo AF: 0.608

Asia WGS AF: 0.725 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4612756; hg19: chr11-93358154;