rs700552

Variant names:

• chr2-169366666-C-G
• rs700552

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 0.584 in 152,072 control chromosomes in the GnomAD database, including 26,490 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 0.58 (26490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 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: 0.585 AC: 88837 AN: 151954 Hom.: 26476 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.584 AC: 88884 AN: 152072 Hom.: 26490 Cov.: 32 AF XY: 0.581 AC XY: 43170 AN XY: 74348

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.588

Alfa AF: 0.624 Hom.: 16746

Bravo AF: 0.579

Asia WGS AF: 0.445 AC: 1549 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	1.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs700552; hg19: chr2-170223176;