rs1183205

Positions:

• chr1-233684653-C-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 0.261 in 152,002 control chromosomes in the GnomAD database, including 5,470 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 0.26 (5470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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: 0.261 AC: 39612 AN: 151884 Hom.: 5468 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.261 AC: 39637 AN: 152002 Hom.: 5470 Cov.: 31 AF XY: 0.258 AC XY: 19180 AN XY: 74278

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.266

Alfa AF: 0.293 Hom.: 814

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1091564; hg19: chr1-233820399;