rs1424954

Positions:

• chr2-147843225-G-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 0.325 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;