11-44517557-A-G

Variant names:

• chr11-44517557-A-G
• rs11038042

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.34 (2620 hom., cov: 17)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 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: 0.339 AC: 25945 AN: 76562 Hom.: 2621 Cov.: 17

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.505

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.339 AC: 25960 AN: 76614 Hom.: 2620 Cov.: 17 AF XY: 0.340 AC XY: 12673 AN XY: 37234

African (AFR) AF: 0.201 AC: 3174 AN: 15820

American (AMR) AF: 0.375 AC: 3024 AN: 8060

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1212 AN: 2420

East Asian (EAS) AF: 0.405 AC: 742 AN: 1832

South Asian (SAS) AF: 0.455 AC: 1106 AN: 2430

European-Finnish (FIN) AF: 0.346 AC: 1827 AN: 5286

Middle Eastern (MID) AF: 0.505 AC: 95 AN: 188

European-Non Finnish (NFE) AF: 0.365 AC: 14225 AN: 38946

Other (OTH) AF: 0.350 AC: 407 AN: 1162

Alfa AF: 0.195 Hom.: 4886

Bravo AF: 0.173

Asia WGS AF: 0.200 AC: 692 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.54
PhyloP100		-0.88

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11038042; hg19: chr11-44539107;