rs2070803

chr1-155185239-G-Achr1-155185239-G-Cchr1-155185239-G-T

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 0.549 in 152,112 control chromosomes in the GnomAD database, including 23,407 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 0.55 (23407 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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: 0.549 AC: 83511 AN: 151994 Hom.: 23378 Cov.: 34

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.549 AC: 83584 AN: 152112 Hom.: 23407 Cov.: 34 AF XY: 0.543 AC XY: 40406 AN XY: 74360

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.551

Alfa AF: 0.575 Hom.: 5037

Bravo AF: 0.542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070803; hg19: chr1-155157715;