12-23270928-A-G

Variant names:

• chr12-23270928-A-G
• rs10743465

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.581 AC: 24048 AN: 41418

American (AMR) AF: 0.931 AC: 14184 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3388 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5158 AN: 5168

South Asian (SAS) AF: 0.951 AC: 4581 AN: 4818

European-Finnish (FIN) AF: 0.983 AC: 10433 AN: 10618

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66538 AN: 67986

Other (OTH) AF: 0.892 AC: 1879 AN: 2106

Alfa AF: 0.909 Hom.: 10737

Bravo AF: 0.849

Asia WGS AF: 0.940 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.79
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10743465; hg19: chr12-23423862;