chr1-229373158-T-C

Variant names:

• chr1-229373158-T-C
• rs238099

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;