chr1-226356719-T-C

Position:

• chr1-226356719-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 0.495 in 151,998 control chromosomes in the GnomAD database, including 19,644 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 0.50 (19644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.495 AC: 75238 AN: 151880 Hom.: 19650 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.495 AC: 75256 AN: 151998 Hom.: 19644 Cov.: 32 AF XY: 0.490 AC XY: 36387 AN XY: 74284

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.526

Alfa AF: 0.567 Hom.: 49738

Bravo AF: 0.486

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12567614; hg19: chr1-226544420; COSMIC: COSV64691951;