rs874401

Variant names:

• chr2-25179411-G-A
• rs874401

Your query was ambiguous. Multiple possible variants found:

• chr2-25179411-G-A
• chr2-25179411-G-C

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 0.223 in 152,094 control chromosomes in the GnomAD database, including 4,002 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 0.22 (4002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 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: 0.223 AC: 33827 AN: 151976 Hom.: 3986 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.223 AC: 33878 AN: 152094 Hom.: 4002 Cov.: 32 AF XY: 0.232 AC XY: 17234 AN XY: 74362

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.211

Alfa AF: 0.192 Hom.: 2483

Bravo AF: 0.231

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs874401; hg19: chr2-25402280;