rs1183205

Variant names:

• chr1-233684653-C-T
• rs1091564

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 0.261 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.210 AC: 8689 AN: 41426

American (AMR) AF: 0.213 AC: 3260 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3466

East Asian (EAS) AF: 0.113 AC: 586 AN: 5172

South Asian (SAS) AF: 0.184 AC: 884 AN: 4816

European-Finnish (FIN) AF: 0.346 AC: 3649 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20941 AN: 67968

Other (OTH) AF: 0.266 AC: 563 AN: 2114

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

Other links and lift over

dbSNP: rs1091564; hg19: chr1-233820399;