1-50378501-T-C

Variant names:

• chr1-50378501-T-C
• rs2455636

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 0.798 in 152,028 control chromosomes in the GnomAD database, including 48,756 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 0.80 (48756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.851 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: 0.799 AC: 121337 AN: 151910 Hom.: 48744 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.798 AC: 121389 AN: 152028 Hom.: 48756 Cov.: 31 AF XY: 0.802 AC XY: 59627 AN XY: 74324

African (AFR) AF: 0.699 AC: 28932 AN: 41390

American (AMR) AF: 0.863 AC: 13190 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2771 AN: 3468

East Asian (EAS) AF: 0.832 AC: 4300 AN: 5170

South Asian (SAS) AF: 0.853 AC: 4103 AN: 4808

European-Finnish (FIN) AF: 0.874 AC: 9239 AN: 10576

Middle Eastern (MID) AF: 0.901 AC: 263 AN: 292

European-Non Finnish (NFE) AF: 0.825 AC: 56090 AN: 68016

Other (OTH) AF: 0.818 AC: 1728 AN: 2112

Alfa AF: 0.812 Hom.: 60669

Bravo AF: 0.792

Asia WGS AF: 0.803 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2455636; hg19: chr1-50844173;