rs1562388

Variant names:

• chr1-159601257-G-C
• rs1562388

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 0.536 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
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.583 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: 0.536 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

African (AFR) AF: 0.489 AC: 20234 AN: 41414

American (AMR) AF: 0.563 AC: 8601 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1945 AN: 3466

East Asian (EAS) AF: 0.151 AC: 776 AN: 5154

South Asian (SAS) AF: 0.471 AC: 2268 AN: 4814

European-Finnish (FIN) AF: 0.550 AC: 5792 AN: 10540

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39893 AN: 67914

Other (OTH) AF: 0.575 AC: 1216 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs1562388; hg19: chr1-159571047;