1-55033276-C-T

Variant names:

• chr1-55033276-C-T
• rs7523242

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 0.199 in 152,058 control chromosomes in the GnomAD database, including 3,852 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 0.20 (3852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30210 AN: 151938 Hom.: 3843 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.199 AC: 30252 AN: 152058 Hom.: 3852 Cov.: 32 AF XY: 0.199 AC XY: 14823 AN XY: 74320

African (AFR) AF: 0.157 AC: 6506 AN: 41480

American (AMR) AF: 0.281 AC: 4291 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3339 AN: 5128

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4820

European-Finnish (FIN) AF: 0.0975 AC: 1033 AN: 10594

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12433 AN: 67964

Other (OTH) AF: 0.232 AC: 490 AN: 2110

Alfa AF: 0.215 Hom.: 1622

Bravo AF: 0.215

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.5
DANN	Benign	0.76
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7523242; hg19: chr1-55498949;