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. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.235 AC: 9767 AN: 41488

American (AMR) AF: 0.351 AC: 5375 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3466

East Asian (EAS) AF: 0.193 AC: 996 AN: 5166

South Asian (SAS) AF: 0.185 AC: 890 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3039 AN: 10568

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12670 AN: 67976

Other (OTH) AF: 0.211 AC: 447 AN: 2114

Alfa AF: 0.198 Hom.: 3426

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs874401; hg19: chr2-25402280;