rs4129991

chr12-23295965-G-Achr12-23295965-G-C

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 0.862 in 152,174 control chromosomes in the GnomAD database, including 59,009 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 0.86 (59009 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131173 AN: 152058 Hom.: 58991 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.978

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.862 AC: 131227 AN: 152174 Hom.: 59009 Cov.: 32 AF XY: 0.866 AC XY: 64412 AN XY: 74414

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.978

Gnomad4 OTH AF: 0.885

Alfa AF: 0.927 Hom.: 14056

Bravo AF: 0.846

Asia WGS AF: 0.941 AC: 3270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.13
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129991; hg19: chr12-23448899;