rs1424954

Variant names:

• chr2-147843225-G-A
• rs1424954

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 0.325 in 152,036 control chromosomes in the GnomAD database, including 8,279 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 (8279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 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: 0.325 AC: 49399 AN: 151920 Hom.: 8274 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.325 AC: 49447 AN: 152036 Hom.: 8279 Cov.: 32 AF XY: 0.327 AC XY: 24303 AN XY: 74298

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.346

Alfa AF: 0.322 Hom.: 977

Bravo AF: 0.333

Asia WGS AF: 0.354 AC: 1233 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.77
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424954; hg19: chr2-148600794;