rs11945798

Variant names:

• chr4-12767608-T-C
• rs11945798

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 0.0852 in 151,844 control chromosomes in the GnomAD database, including 992 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 0.085 (992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.0850 AC: 12902 AN: 151708 Hom.: 990 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0784

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0852 AC: 12932 AN: 151844 Hom.: 992 Cov.: 32 AF XY: 0.0835 AC XY: 6201 AN XY: 74234

African (AFR) AF: 0.204 AC: 8486 AN: 41508

American (AMR) AF: 0.0569 AC: 869 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3470

East Asian (EAS) AF: 0.0242 AC: 125 AN: 5172

South Asian (SAS) AF: 0.0632 AC: 304 AN: 4810

European-Finnish (FIN) AF: 0.0360 AC: 381 AN: 10576

Middle Eastern (MID) AF: 0.0800 AC: 16 AN: 200

European-Non Finnish (NFE) AF: 0.0363 AC: 2462 AN: 67838

Other (OTH) AF: 0.0796 AC: 166 AN: 2086

Alfa AF: 0.0744 Hom.: 95

Bravo AF: 0.0915

Asia WGS AF: 0.0450 AC: 154 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs11945798; hg19: chr4-12769232;