1-226413434-T-C

Position:

• chr1-226413434-T-C

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 0.453 in 152,036 control chromosomes in the GnomAD database, including 17,179 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 0.45 (17179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68704 AN: 151916 Hom.: 17144 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.453 AC: 68804 AN: 152036 Hom.: 17179 Cov.: 32 AF XY: 0.456 AC XY: 33926 AN XY: 74320

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.409

Alfa AF: 0.339 Hom.: 4539

Bravo AF: 0.469

Asia WGS AF: 0.546 AC: 1904 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	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2249844; hg19: chr1-226601135;