rs2880414

Variant names:

• chr4-155172499-A-C
• rs2880414

Your query was ambiguous. Multiple possible variants found:

• chr4-155172499-A-C
• chr4-155172499-A-T

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 0.406 in 151,530 control chromosomes in the GnomAD database, including 14,740 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 0.41 (14740 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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: 0.406 AC: 61488 AN: 151410 Hom.: 14709 Cov.: 30

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.406 AC: 61566 AN: 151530 Hom.: 14740 Cov.: 30 AF XY: 0.412 AC XY: 30500 AN XY: 73970

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.387

Alfa AF: 0.286 Hom.: 13410

Bravo AF: 0.416

Asia WGS AF: 0.425 AC: 1477 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.72
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2880414; hg19: chr4-156093651;