4-60096703-C-T

Variant names:

• chr4-60096703-C-T
• rs1372206

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 0.92 in 152,234 control chromosomes in the GnomAD database, including 64,587 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 0.92 (64587 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.95 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: 0.920 AC: 139963 AN: 152116 Hom.: 64546 Cov.: 33

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.920 AC: 140052 AN: 152234 Hom.: 64587 Cov.: 33 AF XY: 0.922 AC XY: 68612 AN XY: 74432

African (AFR) AF: 0.842 AC: 34968 AN: 41508

American (AMR) AF: 0.963 AC: 14730 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3190 AN: 3468

East Asian (EAS) AF: 0.912 AC: 4715 AN: 5168

South Asian (SAS) AF: 0.892 AC: 4306 AN: 4830

European-Finnish (FIN) AF: 0.970 AC: 10310 AN: 10626

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.952 AC: 64720 AN: 68018

Other (OTH) AF: 0.923 AC: 1952 AN: 2114

Alfa AF: 0.940 Hom.: 47066

Bravo AF: 0.916

Asia WGS AF: 0.902 AC: 3138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.059
DANN	Benign	0.94
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1372206; hg19: chr4-60962421;