4-122447361-C-T

Variant names:

• chr4-122447361-C-T
• rs10027390

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 0.765 in 152,172 control chromosomes in the GnomAD database, including 44,719 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 0.76 (44719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.765 AC: 116267 AN: 152054 Hom.: 44675 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.765 AC: 116368 AN: 152172 Hom.: 44719 Cov.: 32 AF XY: 0.774 AC XY: 57605 AN XY: 74402

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.755

Alfa AF: 0.729 Hom.: 38932

Bravo AF: 0.760

Asia WGS AF: 0.826 AC: 2871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10027390; hg19: chr4-123368516;