7-45923515-C-T

Variant names:

• chr7-45923515-C-T
• rs924140

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 0.487 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
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.578 AC: 23947 AN: 41460

American (AMR) AF: 0.374 AC: 5710 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3466

East Asian (EAS) AF: 0.754 AC: 3886 AN: 5156

South Asian (SAS) AF: 0.444 AC: 2133 AN: 4804

European-Finnish (FIN) AF: 0.380 AC: 4002 AN: 10534

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30812 AN: 67952

Other (OTH) AF: 0.478 AC: 1009 AN: 2110

Alfa AF: 0.473 Hom.: 40126

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs924140; hg19: chr7-45963114;