chr1-226420403-C-A

Variant names:

• chr1-226420403-C-A
• rs1858550

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 0.443 in 151,934 control chromosomes in the GnomAD database, including 16,144 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 0.44 (16144 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.443 AC: 67228 AN: 151816 Hom.: 16126 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.443 AC: 67301 AN: 151934 Hom.: 16144 Cov.: 31 AF XY: 0.447 AC XY: 33209 AN XY: 74252

African (AFR) AF: 0.593 AC: 24548 AN: 41422

American (AMR) AF: 0.463 AC: 7064 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1057 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4122 AN: 5158

South Asian (SAS) AF: 0.375 AC: 1801 AN: 4804

European-Finnish (FIN) AF: 0.434 AC: 4579 AN: 10548

Middle Eastern (MID) AF: 0.343 AC: 98 AN: 286

European-Non Finnish (NFE) AF: 0.338 AC: 22975 AN: 67950

Other (OTH) AF: 0.406 AC: 860 AN: 2116

Alfa AF: 0.391 Hom.: 1521

Bravo AF: 0.456

Asia WGS AF: 0.542 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1858550; hg19: chr1-226608104;