chr7-134283992-A-T

Variant names:

• chr7-134283992-A-T
• rs1421483

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.949 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

Gnomad4 AFR AF: 0.986

Gnomad4 AMR AF: 0.942

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 0.959

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.926

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1421483; hg19: chr7-133968744;