rs1920748

Variant names:

• chr12-91005279-C-T
• rs1920748

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 0.88 in 152,024 control chromosomes in the GnomAD database, including 58,864 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 0.88 (58864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.924 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: 0.880 AC: 133649 AN: 151906 Hom.: 58825 Cov.: 32

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.843

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.880 AC: 133739 AN: 152024 Hom.: 58864 Cov.: 32 AF XY: 0.884 AC XY: 65628 AN XY: 74254

African (AFR) AF: 0.831 AC: 34455 AN: 41454

American (AMR) AF: 0.907 AC: 13832 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3037 AN: 3468

East Asian (EAS) AF: 0.929 AC: 4784 AN: 5150

South Asian (SAS) AF: 0.947 AC: 4568 AN: 4824

European-Finnish (FIN) AF: 0.932 AC: 9878 AN: 10594

Middle Eastern (MID) AF: 0.845 AC: 245 AN: 290

European-Non Finnish (NFE) AF: 0.888 AC: 60388 AN: 67976

Other (OTH) AF: 0.872 AC: 1844 AN: 2114

Alfa AF: 0.881 Hom.: 8467

Bravo AF: 0.875

Asia WGS AF: 0.936 AC: 3248 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.44
PhyloP100		0.84
PromoterAI		0.026	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1920748; hg19: chr12-91399056;