chr7-54121396-A-G

Position:

• chr7-54121396-A-G

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54121396A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.686

Alfa AF: 0.708 Hom.: 69834

Bravo AF: 0.623

Asia WGS AF: 0.680 AC: 2364 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2330668; hg19: chr7-54189089;