7-54708949-A-T

Variant names:

• chr7-54708949-A-T
• rs1823899

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 0.688 in 152,134 control chromosomes in the GnomAD database, including 37,030 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 0.69 (37030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104513 AN: 152016 Hom.: 36982 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.688 AC: 104620 AN: 152134 Hom.: 37030 Cov.: 32 AF XY: 0.683 AC XY: 50774 AN XY: 74380

African (AFR) AF: 0.855 AC: 35481 AN: 41520

American (AMR) AF: 0.574 AC: 8770 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2567 AN: 3472

East Asian (EAS) AF: 0.405 AC: 2099 AN: 5184

South Asian (SAS) AF: 0.668 AC: 3223 AN: 4822

European-Finnish (FIN) AF: 0.652 AC: 6898 AN: 10572

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43377 AN: 67966

Other (OTH) AF: 0.689 AC: 1455 AN: 2112

Alfa AF: 0.665 Hom.: 4266

Bravo AF: 0.690

Asia WGS AF: 0.573 AC: 1994 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.52
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1823899; hg19: chr7-54776642;