1-245133143-C-T

Variant names:

• chr1-245133143-C-T
• rs12407427

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 0.217 in 152,000 control chromosomes in the GnomAD database, including 4,784 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 0.22 (4784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.217 AC: 32956 AN: 151882 Hom.: 4751 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.217 AC: 33047 AN: 152000 Hom.: 4784 Cov.: 32 AF XY: 0.218 AC XY: 16192 AN XY: 74324

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.222

Alfa AF: 0.163 Hom.: 1870

Bravo AF: 0.249

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12407427; hg19: chr1-245296445;