5-7923570-C-T

Position:

• chr5-7923570-C-T

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 0.663 in 151,930 control chromosomes in the GnomAD database, including 33,722 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 0.66 (33722 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7923570C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100565 AN: 151810 Hom.: 33675 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.663 AC: 100669 AN: 151930 Hom.: 33722 Cov.: 31 AF XY: 0.662 AC XY: 49168 AN XY: 74250

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.603

Alfa AF: 0.632 Hom.: 30252

Bravo AF: 0.666

Asia WGS AF: 0.493 AC: 1711 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs327575; hg19: chr5-7923683;