chr1-233561784-C-T

Variant names:

• chr1-233561784-C-T
• rs780245

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 0.127 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0398 AC: 1647 AN: 41334

American (AMR) AF: 0.110 AC: 1677 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3472

East Asian (EAS) AF: 0.133 AC: 690 AN: 5182

South Asian (SAS) AF: 0.120 AC: 579 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1682 AN: 10566

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12097 AN: 67994

Other (OTH) AF: 0.136 AC: 287 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.2
DANN	Benign	0.84
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs780245; hg19: chr1-233697530;