rs704144

Positions:

• chr12-91258901-G-A
• chr12-91258901-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 0.832 in 151,284 control chromosomes in the GnomAD database, including 52,973 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 0.83 (52973 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.832 AC: 125845 AN: 151172 Hom.: 52955 Cov.: 27

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.832 AC: 125914 AN: 151284 Hom.: 52973 Cov.: 27 AF XY: 0.837 AC XY: 61875 AN XY: 73926

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.931

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.834

Alfa AF: 0.876 Hom.: 93282

Bravo AF: 0.818

Asia WGS AF: 0.875 AC: 3038 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs704144; hg19: chr12-91652678;