chr1-48048827-C-T

Variant names:

• chr1-48048827-C-T
• rs823385

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 0.617 in 151,912 control chromosomes in the GnomAD database, including 29,234 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 0.62 (29234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93610 AN: 151794 Hom.: 29188 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.617 AC: 93718 AN: 151912 Hom.: 29234 Cov.: 32 AF XY: 0.621 AC XY: 46088 AN XY: 74254

African (AFR) AF: 0.688 AC: 28512 AN: 41442

American (AMR) AF: 0.627 AC: 9573 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3163 AN: 5116

South Asian (SAS) AF: 0.615 AC: 2961 AN: 4816

European-Finnish (FIN) AF: 0.625 AC: 6596 AN: 10558

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38801 AN: 67924

Other (OTH) AF: 0.624 AC: 1316 AN: 2108

Alfa AF: 0.591 Hom.: 10327

Bravo AF: 0.614

Asia WGS AF: 0.593 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.72
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs823385; hg19: chr1-48514499; COSMIC: COSV71762804;