rs1562388

Variant names:

• chr1-159601257-G-C
• rs1562388

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 0.536 in 151,908 control chromosomes in the GnomAD database, including 22,449 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 (22449 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

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 (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81419 AN: 151790 Hom.: 22430 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.536 AC: 81486 AN: 151908 Hom.: 22449 Cov.: 31 AF XY: 0.532 AC XY: 39485 AN XY: 74254

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.575

Alfa AF: 0.567 Hom.: 3069

Bravo AF: 0.535

Asia WGS AF: 0.305 AC: 1064 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	1.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562388; hg19: chr1-159571047;