chr12-21998639-C-T

Variant names:

• chr12-21998639-C-T
• rs10743430

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 0.775 in 152,094 control chromosomes in the GnomAD database, including 51,293 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 0.78 (51293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.776 AC: 117858 AN: 151976 Hom.: 51280 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.775 AC: 117898 AN: 152094 Hom.: 51293 Cov.: 32 AF XY: 0.783 AC XY: 58222 AN XY: 74376

African (AFR) AF: 0.339 AC: 14057 AN: 41406

American (AMR) AF: 0.889 AC: 13573 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3077 AN: 3472

East Asian (EAS) AF: 0.989 AC: 5120 AN: 5178

South Asian (SAS) AF: 0.909 AC: 4388 AN: 4828

European-Finnish (FIN) AF: 0.978 AC: 10387 AN: 10616

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64572 AN: 68008

Other (OTH) AF: 0.806 AC: 1700 AN: 2108

Alfa AF: 0.890 Hom.: 211823

Bravo AF: 0.750

Asia WGS AF: 0.908 AC: 3155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.44
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10743430; hg19: chr12-22151573;