1-194485568-G-T

Position:

• chr1-194485568-G-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 0.931 in 151,138 control chromosomes in the GnomAD database, including 65,565 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 0.93 (65565 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.194485568G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.930 AC: 140521 AN: 151020 Hom.: 65501 Cov.: 31

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.931 AC: 140644 AN: 151138 Hom.: 65565 Cov.: 31 AF XY: 0.931 AC XY: 68741 AN XY: 73870

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.943

Alfa AF: 0.905 Hom.: 21689

Bravo AF: 0.938

Asia WGS AF: 0.974 AC: 3382 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.60
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494354; hg19: chr1-194454698;