7-134283992-A-T

Variant names:

• chr7-134283992-A-T
• rs1421483

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.949 in 152,298 control chromosomes in the GnomAD database, including 68,603 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 0.95 (68603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 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: 0.949 AC: 144356 AN: 152180 Hom.: 68541 Cov.: 31

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.949 AC: 144478 AN: 152298 Hom.: 68603 Cov.: 31 AF XY: 0.952 AC XY: 70870 AN XY: 74458

African (AFR) AF: 0.986 AC: 41018 AN: 41582

American (AMR) AF: 0.942 AC: 14405 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3141 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5165 AN: 5168

South Asian (SAS) AF: 0.978 AC: 4720 AN: 4824

European-Finnish (FIN) AF: 0.959 AC: 10178 AN: 10616

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62737 AN: 68026

Other (OTH) AF: 0.926 AC: 1955 AN: 2112

Alfa AF: 0.929 Hom.: 3603

Bravo AF: 0.949

Asia WGS AF: 0.988 AC: 3436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	9.2
DANN	Benign	0.67
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1421483; hg19: chr7-133968744;