rs1424954

Variant names:

• chr2-147843225-G-A
• rs1424954

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.297 AC: 12327 AN: 41476

American (AMR) AF: 0.381 AC: 5822 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2650 AN: 5164

South Asian (SAS) AF: 0.318 AC: 1532 AN: 4818

European-Finnish (FIN) AF: 0.335 AC: 3534 AN: 10564

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21343 AN: 67952

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.321 Hom.: 1014

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1424954; hg19: chr2-148600794;