1-55030322-T-C

Variant names:

• chr1-55030322-T-C
• rs2495497

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 0.861 in 152,182 control chromosomes in the GnomAD database, including 57,109 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 0.86 (57109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.94 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: 0.861 AC: 130911 AN: 152064 Hom.: 57070 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.861 AC: 130999 AN: 152182 Hom.: 57109 Cov.: 32 AF XY: 0.856 AC XY: 63655 AN XY: 74378

African (AFR) AF: 0.948 AC: 39372 AN: 41550

American (AMR) AF: 0.743 AC: 11357 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2780 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2512 AN: 5154

South Asian (SAS) AF: 0.808 AC: 3896 AN: 4820

European-Finnish (FIN) AF: 0.835 AC: 8837 AN: 10578

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59396 AN: 68014

Other (OTH) AF: 0.836 AC: 1763 AN: 2108

Alfa AF: 0.857 Hom.: 26676

Bravo AF: 0.851

Asia WGS AF: 0.666 AC: 2316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2495497; hg19: chr1-55495995;