12-23270928-A-G

Variant names:

• chr12-23270928-A-G
• rs10743465

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 0.864 in 152,028 control chromosomes in the GnomAD database, including 59,103 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 (59103 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.864 AC: 131290 AN: 151910 Hom.: 59088 Cov.: 31

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.864 AC: 131339 AN: 152028 Hom.: 59103 Cov.: 31 AF XY: 0.867 AC XY: 64424 AN XY: 74314

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.892

Alfa AF: 0.919 Hom.: 10598

Bravo AF: 0.849

Asia WGS AF: 0.940 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10743465; hg19: chr12-23423862;