1-214781596-T-C

Position:

• chr1-214781596-T-C

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 0.528 in 151,862 control chromosomes in the GnomAD database, including 21,796 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 0.53 (21796 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.214781596T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80172 AN: 151742 Hom.: 21772 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.528 AC: 80251 AN: 151862 Hom.: 21796 Cov.: 31 AF XY: 0.541 AC XY: 40096 AN XY: 74170

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.496

Alfa AF: 0.497 Hom.: 3056

Bravo AF: 0.526

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6695352; hg19: chr1-214954939;