chr1-228184361-C-T

Variant names:

• chr1-228184361-C-T
• rs1059778

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 0.363 in 152,080 control chromosomes in the GnomAD database, including 10,269 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 0.36 (10269 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 15 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 = 0.394 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: 0.363 AC: 55212 AN: 151962 Hom.: 10256 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.363 AC: 55261 AN: 152080 Hom.: 10269 Cov.: 33 AF XY: 0.360 AC XY: 26723 AN XY: 74330

African (AFR) AF: 0.309 AC: 12822 AN: 41510

American (AMR) AF: 0.377 AC: 5758 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1432 AN: 3472

East Asian (EAS) AF: 0.408 AC: 2107 AN: 5164

South Asian (SAS) AF: 0.301 AC: 1450 AN: 4814

European-Finnish (FIN) AF: 0.347 AC: 3671 AN: 10570

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26857 AN: 67960

Other (OTH) AF: 0.368 AC: 777 AN: 2110

Alfa AF: 0.380 Hom.: 20779

Bravo AF: 0.367

Asia WGS AF: 0.325 AC: 1128 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	0.060
DANN	Benign	0.58
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1059778; hg19: chr1-228372062;