rs871799

Positions:

• chr1-203200743-C-G

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 0.181 in 152,100 control chromosomes in the GnomAD database, including 3,250 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 0.18 (3250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 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: 0.181 AC: 27493 AN: 151982 Hom.: 3237 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.181 AC: 27542 AN: 152100 Hom.: 3250 Cov.: 32 AF XY: 0.183 AC XY: 13620 AN XY: 74350

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.0481

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.211

Alfa AF: 0.140 Hom.: 248

Bravo AF: 0.204

Asia WGS AF: 0.307 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs871799; hg19: chr1-203169871;