rs1920748

Variant names:

• chr12-91005279-C-T
• rs1920748

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 0.88 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.880 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

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.872

Alfa AF: 0.883 Hom.: 8188

Bravo AF: 0.875

Asia WGS AF: 0.936 AC: 3248 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1920748; hg19: chr12-91399056;