4-44607167-C-T

Variant names:

• chr4-44607167-C-T
• rs1439358

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 0.757 in 152,114 control chromosomes in the GnomAD database, including 44,160 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 (44160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115016 AN: 151996 Hom.: 44148 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.757 AC: 115078 AN: 152114 Hom.: 44160 Cov.: 32 AF XY: 0.756 AC XY: 56212 AN XY: 74332

African (AFR) AF: 0.627 AC: 25999 AN: 41474

American (AMR) AF: 0.716 AC: 10928 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2718 AN: 3472

East Asian (EAS) AF: 0.823 AC: 4257 AN: 5170

South Asian (SAS) AF: 0.798 AC: 3840 AN: 4812

European-Finnish (FIN) AF: 0.845 AC: 8951 AN: 10594

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55817 AN: 68002

Other (OTH) AF: 0.756 AC: 1599 AN: 2116

Alfa AF: 0.778 Hom.: 6032

Bravo AF: 0.740

Asia WGS AF: 0.734 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1439358; hg19: chr4-44609184;