5-7923570-C-T

Variant names:

• chr5-7923570-C-T
• rs327575

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 0.663 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.728 AC: 30174 AN: 41426

American (AMR) AF: 0.689 AC: 10528 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1885 AN: 3468

East Asian (EAS) AF: 0.522 AC: 2684 AN: 5142

South Asian (SAS) AF: 0.502 AC: 2412 AN: 4804

European-Finnish (FIN) AF: 0.686 AC: 7234 AN: 10542

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.643 AC: 43702 AN: 67960

Other (OTH) AF: 0.603 AC: 1270 AN: 2106

Alfa AF: 0.634 Hom.: 41044

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs327575; hg19: chr5-7923683;