1-208798618-C-T

Position:

• chr1-208798618-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 0.842 in 152,140 control chromosomes in the GnomAD database, including 54,778 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 0.84 (54778 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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 (SAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.208798618C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128047 AN: 152022 Hom.: 54738 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.842 AC: 128137 AN: 152140 Hom.: 54778 Cov.: 31 AF XY: 0.847 AC XY: 63003 AN XY: 74388

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.882

Alfa AF: 0.891 Hom.: 77727

Bravo AF: 0.837

Asia WGS AF: 0.931 AC: 3238 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	0.092
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1182870; hg19: chr1-208971963;