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. Variant got -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

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 (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0886

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.100

Alfa AF: 0.118 Hom.: 1474

Bravo AF: 0.104

Asia WGS AF: 0.0880 AC: 306 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	0.96
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11170890; hg19: chr12-39549189;