7-45923515-C-T

Variant names:

• chr7-45923515-C-T
• rs924140

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 0.487 in 151,964 control chromosomes in the GnomAD database, including 18,591 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 0.49 (18591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73989 AN: 151846 Hom.: 18597 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.487 AC: 74006 AN: 151964 Hom.: 18591 Cov.: 32 AF XY: 0.482 AC XY: 35786 AN XY: 74272

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.478

Alfa AF: 0.470 Hom.: 21638

Bravo AF: 0.493

Asia WGS AF: 0.538 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924140; hg19: chr7-45963114;