7-54121396-A-G

Variant names:

• chr7-54121396-A-G
• rs2330668

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 0.63 in 151,824 control chromosomes in the GnomAD database, including 31,449 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 0.63 (31449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.631 AC: 95696 AN: 151710 Hom.: 31453 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.630 AC: 95720 AN: 151824 Hom.: 31449 Cov.: 32 AF XY: 0.627 AC XY: 46500 AN XY: 74196

African (AFR) AF: 0.446 AC: 18418 AN: 41254

American (AMR) AF: 0.649 AC: 9904 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2694 AN: 3470

East Asian (EAS) AF: 0.754 AC: 3884 AN: 5152

South Asian (SAS) AF: 0.697 AC: 3359 AN: 4816

European-Finnish (FIN) AF: 0.641 AC: 6776 AN: 10564

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.711 AC: 48349 AN: 67986

Other (OTH) AF: 0.686 AC: 1452 AN: 2116

Alfa AF: 0.693 Hom.: 101386

Bravo AF: 0.623

Asia WGS AF: 0.680 AC: 2364 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.72
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs2330668; hg19: chr7-54189089;