1-226420403-C-A

Position:

• chr1-226420403-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.406

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1858550; hg19: chr1-226608104;