1-12624318-C-T

Position:

• chr1-12624318-C-T

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 0.097 in 151,934 control chromosomes in the GnomAD database, including 1,441 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 0.097 (1441 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12624318C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14693 AN: 151816 Hom.: 1432 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.00945

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0776

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

GnomAD4 genome AF: 0.0970 AC: 14737 AN: 151934 Hom.: 1441 Cov.: 31 AF XY: 0.0936 AC XY: 6954 AN XY: 74260

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.0465

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0823

Gnomad4 FIN AF: 0.00945

Gnomad4 NFE AF: 0.0385

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0473 Hom.: 389

Bravo AF: 0.105

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3010931; hg19: chr1-12684324;