7-53146978-A-G

Position:

• chr7-53146978-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 0.842 in 144,586 control chromosomes in the GnomAD database, including 51,891 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 0.84 (51891 hom., cov: 25)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53146978A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.842 AC: 121713 AN: 144532 Hom.: 51863 Cov.: 25

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.824

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.842 AC: 121769 AN: 144586 Hom.: 51891 Cov.: 25 AF XY: 0.843 AC XY: 59158 AN XY: 70182

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.850

Alfa AF: 0.819 Hom.: 5383

Asia WGS AF: 0.898 AC: 3018 AN: 3364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1357963; hg19: chr7-53214671;