7-45939424-T-G

Variant names:

• chr7-45939424-T-G
• rs1496499

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 0.525 in 151,998 control chromosomes in the GnomAD database, including 21,712 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 0.52 (21712 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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: 0.525 AC: 79691 AN: 151880 Hom.: 21713 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.524 AC: 79723 AN: 151998 Hom.: 21712 Cov.: 31 AF XY: 0.525 AC XY: 39030 AN XY: 74300

African (AFR) AF: 0.624 AC: 25846 AN: 41432

American (AMR) AF: 0.525 AC: 8025 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3468

East Asian (EAS) AF: 0.891 AC: 4606 AN: 5168

South Asian (SAS) AF: 0.547 AC: 2632 AN: 4816

European-Finnish (FIN) AF: 0.381 AC: 4023 AN: 10564

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

European-Non Finnish (NFE) AF: 0.456 AC: 31016 AN: 67962

Other (OTH) AF: 0.510 AC: 1072 AN: 2104

Alfa AF: 0.490 Hom.: 35293

Bravo AF: 0.541

Asia WGS AF: 0.665 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	13
DANN	Benign	0.95
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1496499; hg19: chr7-45979023;