4-122447361-C-T

Variant names:

• chr4-122447361-C-T
• rs10027390

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 0.765 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.787 AC: 32673 AN: 41512

American (AMR) AF: 0.804 AC: 12297 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2436 AN: 3466

East Asian (EAS) AF: 0.863 AC: 4474 AN: 5186

South Asian (SAS) AF: 0.836 AC: 4033 AN: 4824

European-Finnish (FIN) AF: 0.860 AC: 9110 AN: 10598

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48983 AN: 67974

Other (OTH) AF: 0.755 AC: 1593 AN: 2110

Alfa AF: 0.730 Hom.: 47225

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
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs10027390; hg19: chr4-123368516;