rs11170890

Variant names:

• chr12-39155387-G-A
• rs11170890

Your query was ambiguous. Multiple possible variants found:

• chr12-39155387-G-A
• chr12-39155387-G-T

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 0.111 in 151,918 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 0.11 (992 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16829 AN: 151802 Hom.: 989 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.111 AC: 16845 AN: 151918 Hom.: 992 Cov.: 31 AF XY: 0.111 AC XY: 8233 AN XY: 74234

African (AFR) AF: 0.101 AC: 4166 AN: 41406

American (AMR) AF: 0.0689 AC: 1052 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.0886 AC: 457 AN: 5160

South Asian (SAS) AF: 0.101 AC: 485 AN: 4810

European-Finnish (FIN) AF: 0.143 AC: 1505 AN: 10540

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8516 AN: 67958

Other (OTH) AF: 0.100 AC: 211 AN: 2102

Alfa AF: 0.118 Hom.: 1739

Bravo AF: 0.104

Asia WGS AF: 0.0880 AC: 306 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	0.96
DANN	Benign	0.78
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs11170890; hg19: chr12-39549189;