1-58776356-A-C

Variant names:

• chr1-58776356-A-C
• rs2760496

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 0.264 in 151,912 control chromosomes in the GnomAD database, including 5,922 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 0.26 (5922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 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: 0.264 AC: 40015 AN: 151794 Hom.: 5912 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.264 AC: 40059 AN: 151912 Hom.: 5922 Cov.: 32 AF XY: 0.276 AC XY: 20461 AN XY: 74222

African (AFR) AF: 0.157 AC: 6490 AN: 41440

American (AMR) AF: 0.267 AC: 4078 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3464

East Asian (EAS) AF: 0.503 AC: 2599 AN: 5164

South Asian (SAS) AF: 0.509 AC: 2448 AN: 4810

European-Finnish (FIN) AF: 0.348 AC: 3660 AN: 10514

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18773 AN: 67928

Other (OTH) AF: 0.285 AC: 602 AN: 2112

Alfa AF: 0.264 Hom.: 7187

Bravo AF: 0.253

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.080
DANN	Benign	0.76
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2760496; hg19: chr1-59242028;