rs1614148

Positions:

• chr1-231462218-C-A

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 0.238 in 152,114 control chromosomes in the GnomAD database, including 4,573 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 0.24 (4573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.299 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: 0.238 AC: 36127 AN: 151996 Hom.: 4568 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.238 AC: 36144 AN: 152114 Hom.: 4573 Cov.: 32 AF XY: 0.230 AC XY: 17079 AN XY: 74344

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0359

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.233

Alfa AF: 0.265 Hom.: 5433

Bravo AF: 0.252

Asia WGS AF: 0.0880 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1614148; hg19: chr1-231597964;