rs4574118

Variant names:

• chr2-106331987-C-G
• rs4574118

Your query was ambiguous. Multiple possible variants found:

• chr2-106331987-C-G
• chr2-106331987-C-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 0.841 in 152,180 control chromosomes in the GnomAD database, including 53,897 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 0.84 (53897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.841 AC: 127814 AN: 152062 Hom.: 53849 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.841 AC: 127922 AN: 152180 Hom.: 53897 Cov.: 32 AF XY: 0.846 AC XY: 62927 AN XY: 74402

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.824

Alfa AF: 0.826 Hom.: 6450

Bravo AF: 0.839

Asia WGS AF: 0.936 AC: 3254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4574118; hg19: chr2-106948443;