chr4-101372387-C-T

Variant names:

• chr4-101372387-C-T
• rs1822168

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 0.723 in 151,952 control chromosomes in the GnomAD database, including 40,271 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 0.72 (40271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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: 0.723 AC: 109781 AN: 151834 Hom.: 40250 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.723 AC: 109844 AN: 151952 Hom.: 40271 Cov.: 31 AF XY: 0.711 AC XY: 52803 AN XY: 74254

African (AFR) AF: 0.820 AC: 34031 AN: 41484

American (AMR) AF: 0.629 AC: 9589 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2506 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2577 AN: 5154

South Asian (SAS) AF: 0.590 AC: 2843 AN: 4816

European-Finnish (FIN) AF: 0.628 AC: 6609 AN: 10526

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49415 AN: 67940

Other (OTH) AF: 0.718 AC: 1511 AN: 2104

Alfa AF: 0.717 Hom.: 19830

Bravo AF: 0.727

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.26
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1822168; hg19: chr4-102293544;