1-194485568-G-T

Variant names:

• chr1-194485568-G-T
• rs2494354

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.981 AC: 40633 AN: 41432

American (AMR) AF: 0.952 AC: 14353 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3299 AN: 3450

East Asian (EAS) AF: 1.00 AC: 5114 AN: 5116

South Asian (SAS) AF: 0.957 AC: 4607 AN: 4816

European-Finnish (FIN) AF: 0.868 AC: 9174 AN: 10574

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60319 AN: 67368

Other (OTH) AF: 0.943 AC: 1973 AN: 2092

Alfa AF: 0.906 Hom.: 25235

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2494354; hg19: chr1-194454698;