rs704144

Variant names:

• chr12-91258901-G-A
• rs704144

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;