1-23841529-C-T

Variant names:

• chr1-23841529-C-T
• rs12744386

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 0.365 in 152,086 control chromosomes in the GnomAD database, including 10,642 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 0.36 (10642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 30 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 = 0.458 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: 0.365 AC: 55432 AN: 151968 Hom.: 10638 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.365 AC: 55472 AN: 152086 Hom.: 10642 Cov.: 32 AF XY: 0.362 AC XY: 26904 AN XY: 74334

African (AFR) AF: 0.227 AC: 9413 AN: 41510

American (AMR) AF: 0.360 AC: 5495 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1499 AN: 3466

East Asian (EAS) AF: 0.474 AC: 2452 AN: 5172

South Asian (SAS) AF: 0.287 AC: 1386 AN: 4822

European-Finnish (FIN) AF: 0.436 AC: 4601 AN: 10554

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.431 AC: 29298 AN: 67982

Other (OTH) AF: 0.389 AC: 822 AN: 2112

Alfa AF: 0.406 Hom.: 6779

Bravo AF: 0.354

Asia WGS AF: 0.363 AC: 1265 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	5.6
DANN	Benign	0.69
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs12744386; hg19: chr1-24168019;