1-48219763-T-C

Variant names:

• chr1-48219763-T-C
• rs926979

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 0.539 in 152,106 control chromosomes in the GnomAD database, including 25,141 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 0.54 (25141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81967 AN: 151988 Hom.: 25136 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.539 AC: 81987 AN: 152106 Hom.: 25141 Cov.: 32 AF XY: 0.544 AC XY: 40442 AN XY: 74358

African (AFR) AF: 0.226 AC: 9395 AN: 41498

American (AMR) AF: 0.667 AC: 10192 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2148 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4064 AN: 5154

South Asian (SAS) AF: 0.634 AC: 3057 AN: 4822

European-Finnish (FIN) AF: 0.649 AC: 6865 AN: 10584

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44366 AN: 67968

Other (OTH) AF: 0.552 AC: 1165 AN: 2112

Alfa AF: 0.626 Hom.: 51997

Bravo AF: 0.528

Asia WGS AF: 0.686 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.026
DANN	Benign	0.71
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs926979; hg19: chr1-48685435;