rs238102

Variant names:

• chr1-229347401-C-A
• rs238102

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 0.326 in 152,030 control chromosomes in the GnomAD database, including 8,358 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 0.33 (8358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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: 0.326 AC: 49499 AN: 151912 Hom.: 8341 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.326 AC: 49561 AN: 152030 Hom.: 8358 Cov.: 32 AF XY: 0.323 AC XY: 23971 AN XY: 74320

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.339

Alfa AF: 0.305 Hom.: 14711

Bravo AF: 0.338

Asia WGS AF: 0.382 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
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: rs238102; hg19: chr1-229483148; COSMIC: COSV52910428;