1-233561784-C-T

Variant names:

• chr1-233561784-C-T
• rs780245

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 0.127 in 151,942 control chromosomes in the GnomAD database, including 1,527 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 0.13 (1527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 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: 0.127 AC: 19332 AN: 151824 Hom.: 1527 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.127 AC: 19332 AN: 151942 Hom.: 1527 Cov.: 32 AF XY: 0.125 AC XY: 9303 AN XY: 74294

Gnomad4 AFR AF: 0.0398

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.136

Alfa AF: 0.105 Hom.: 212

Bravo AF: 0.117

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs780245; hg19: chr1-233697530;