rs1556557

Variant names:

• chr1-242816714-G-A
• rs1556557

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 0.0606 in 152,138 control chromosomes in the GnomAD database, including 401 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 0.061 (401 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 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: 0.0606 AC: 9220 AN: 152020 Hom.: 399 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0774

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0614

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

GnomAD4 genome AF: 0.0606 AC: 9225 AN: 152138 Hom.: 401 Cov.: 32 AF XY: 0.0639 AC XY: 4756 AN XY: 74374

African (AFR) AF: 0.0458 AC: 1903 AN: 41528

American (AMR) AF: 0.0436 AC: 666 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3468

East Asian (EAS) AF: 0.191 AC: 990 AN: 5170

South Asian (SAS) AF: 0.166 AC: 801 AN: 4814

European-Finnish (FIN) AF: 0.0774 AC: 819 AN: 10578

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0548 AC: 3725 AN: 67986

Other (OTH) AF: 0.0659 AC: 139 AN: 2108

Alfa AF: 0.0612 Hom.: 40

Bravo AF: 0.0539

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1556557; hg19: chr1-242980016; COSMIC: COSV107160614;