chr4-127513179-G-C

Variant names:

• chr4-127513179-G-C
• rs2203374

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 0.849 in 152,164 control chromosomes in the GnomAD database, including 55,072 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 0.85 (55072 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 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: 0.849 AC: 129056 AN: 152046 Hom.: 55007 Cov.: 33

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.849 AC: 129178 AN: 152164 Hom.: 55072 Cov.: 33 AF XY: 0.852 AC XY: 63396 AN XY: 74368

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.850

Alfa AF: 0.827 Hom.: 6498

Bravo AF: 0.856

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2203374; hg19: chr4-128434334;