1-55033072-C-T

Variant names:

• chr1-55033072-C-T
• rs2479415

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 0.49 in 152,000 control chromosomes in the GnomAD database, including 18,919 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 0.49 (18919 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.599 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: 0.491 AC: 74527 AN: 151882 Hom.: 18919 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.490 AC: 74551 AN: 152000 Hom.: 18919 Cov.: 32 AF XY: 0.496 AC XY: 36868 AN XY: 74292

African (AFR) AF: 0.428 AC: 17724 AN: 41436

American (AMR) AF: 0.455 AC: 6952 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3470

East Asian (EAS) AF: 0.155 AC: 805 AN: 5180

South Asian (SAS) AF: 0.618 AC: 2977 AN: 4820

European-Finnish (FIN) AF: 0.650 AC: 6861 AN: 10558

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35918 AN: 67940

Other (OTH) AF: 0.492 AC: 1036 AN: 2106

Alfa AF: 0.469 Hom.: 3527

Bravo AF: 0.465

Asia WGS AF: 0.393 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.88
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs2479415; hg19: chr1-55498745;