rs1368882

Positions:

• chr1-54641346-G-A
• chr1-54641346-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.360

Alfa AF: 0.365 Hom.: 13933

Bravo AF: 0.352

Asia WGS AF: 0.529 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368882; hg19: chr1-55107019;