1-115586350-C-T

Variant names:

• chr1-115586350-C-T
• rs4564142

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 0.228 in 152,136 control chromosomes in the GnomAD database, including 4,320 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 0.23 (4320 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 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: 0.228 AC: 34702 AN: 152018 Hom.: 4318 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.228 AC: 34727 AN: 152136 Hom.: 4320 Cov.: 33 AF XY: 0.239 AC XY: 17743 AN XY: 74354

African (AFR) AF: 0.291 AC: 12090 AN: 41524

American (AMR) AF: 0.232 AC: 3543 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3466

East Asian (EAS) AF: 0.330 AC: 1708 AN: 5170

South Asian (SAS) AF: 0.401 AC: 1938 AN: 4828

European-Finnish (FIN) AF: 0.276 AC: 2910 AN: 10558

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11364 AN: 67992

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.184 Hom.: 2063

Bravo AF: 0.222

Asia WGS AF: 0.359 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4564142; hg19: chr1-116128971;