rs874401

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;