1-225808410-G-A

Variant names:

• chr1-225808410-G-A
• rs4559463

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 0.266 in 152,144 control chromosomes in the GnomAD database, including 5,981 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 0.27 (5981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 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: 0.266 AC: 40510 AN: 152024 Hom.: 5978 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.266 AC: 40529 AN: 152144 Hom.: 5981 Cov.: 32 AF XY: 0.267 AC XY: 19880 AN XY: 74370

African (AFR) AF: 0.144 AC: 5973 AN: 41532

American (AMR) AF: 0.287 AC: 4386 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1088 AN: 5164

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4816

European-Finnish (FIN) AF: 0.343 AC: 3627 AN: 10582

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22358 AN: 67968

Other (OTH) AF: 0.284 AC: 601 AN: 2114

Alfa AF: 0.294 Hom.: 901

Bravo AF: 0.255

Asia WGS AF: 0.246 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.2
DANN	Benign	0.92
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs4559463; hg19: chr1-225996112;