1-229373158-T-C

Position:

• chr1-229373158-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 0.383 in 151,938 control chromosomes in the GnomAD database, including 12,567 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 0.38 (12567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453

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 = 0.693 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: 0.383 AC: 58130 AN: 151820 Hom.: 12571 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.383 AC: 58143 AN: 151938 Hom.: 12567 Cov.: 32 AF XY: 0.387 AC XY: 28737 AN XY: 74226

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.423

Alfa AF: 0.443 Hom.: 27423

Bravo AF: 0.372

Asia WGS AF: 0.591 AC: 2055 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	7.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238099; hg19: chr1-229508905;