rs4612756

Variant names:

• chr11-93624988-A-G
• rs4612756

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 0.596 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.589 AC: 24371 AN: 41390

American (AMR) AF: 0.693 AC: 10562 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2219 AN: 3464

East Asian (EAS) AF: 0.766 AC: 3945 AN: 5148

South Asian (SAS) AF: 0.637 AC: 3066 AN: 4810

European-Finnish (FIN) AF: 0.522 AC: 5498 AN: 10530

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38790 AN: 67932

Other (OTH) AF: 0.596 AC: 1252 AN: 2102

Alfa AF: 0.585 Hom.: 12798

Bravo AF: 0.608

Asia WGS AF: 0.725 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs4612756; hg19: chr11-93358154;