chr1-119873363-T-A

Variant names:

• chr1-119873363-T-A
• rs4659245

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 0.5 in 152,144 control chromosomes in the GnomAD database, including 23,089 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 0.50 (23089 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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: 0.500 AC: 76028 AN: 152026 Hom.: 23095 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.500 AC: 76023 AN: 152144 Hom.: 23089 Cov.: 33 AF XY: 0.503 AC XY: 37393 AN XY: 74380

African (AFR) AF: 0.130 AC: 5383 AN: 41536

American (AMR) AF: 0.566 AC: 8650 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2368 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3900 AN: 5160

South Asian (SAS) AF: 0.540 AC: 2601 AN: 4818

European-Finnish (FIN) AF: 0.649 AC: 6863 AN: 10568

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44244 AN: 67984

Other (OTH) AF: 0.562 AC: 1185 AN: 2108

Alfa AF: 0.556 Hom.: 3256

Bravo AF: 0.483

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs4659245; hg19: chr1-120415986; COSMIC: COSV50683509;