1-54641346-G-A

Variant names:

• chr1-54641346-G-A
• rs1368882

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 0.358 in 151,936 control chromosomes in the GnomAD database, including 10,229 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 0.36 (10229 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.358 AC: 54294 AN: 151816 Hom.: 10221 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.358 AC: 54340 AN: 151936 Hom.: 10229 Cov.: 32 AF XY: 0.366 AC XY: 27199 AN XY: 74252

African (AFR) AF: 0.253 AC: 10495 AN: 41456

American (AMR) AF: 0.442 AC: 6750 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3466

East Asian (EAS) AF: 0.491 AC: 2523 AN: 5142

South Asian (SAS) AF: 0.520 AC: 2507 AN: 4818

European-Finnish (FIN) AF: 0.417 AC: 4400 AN: 10542

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25436 AN: 67944

Other (OTH) AF: 0.360 AC: 758 AN: 2106

Alfa AF: 0.363 Hom.: 17467

Bravo AF: 0.352

Asia WGS AF: 0.529 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.58
PhyloP100		0.37
PromoterAI		-0.048	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1368882; hg19: chr1-55107019;