chr1-188331737-C-T

Variant names:

• chr1-188331737-C-T
• rs4463623

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 0.292 in 151,728 control chromosomes in the GnomAD database, including 6,913 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 0.29 (6913 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 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: 0.292 AC: 44208 AN: 151610 Hom.: 6908 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.292 AC: 44243 AN: 151728 Hom.: 6913 Cov.: 32 AF XY: 0.299 AC XY: 22166 AN XY: 74178

African (AFR) AF: 0.358 AC: 14807 AN: 41398

American (AMR) AF: 0.316 AC: 4800 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3464

East Asian (EAS) AF: 0.502 AC: 2582 AN: 5144

South Asian (SAS) AF: 0.416 AC: 2002 AN: 4814

European-Finnish (FIN) AF: 0.314 AC: 3322 AN: 10568

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14876 AN: 67830

Other (OTH) AF: 0.262 AC: 552 AN: 2106

Alfa AF: 0.244 Hom.: 14269

Bravo AF: 0.294

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.23
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4463623; hg19: chr1-188300868;