chr7-24518668-A-T

Variant names:

• chr7-24518668-A-T
• rs2529080

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 0.0771 in 127,518 control chromosomes in the GnomAD database, including 426 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 0.077 (426 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 9827 AN: 127490 Hom.: 422 Cov.: 24

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0545

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0708

Gnomad EAS AF: 0.00125

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.0632

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0771 AC: 9834 AN: 127518 Hom.: 426 Cov.: 24 AF XY: 0.0765 AC XY: 4573 AN XY: 59802

African (AFR) AF: 0.128 AC: 4343 AN: 33824

American (AMR) AF: 0.0566 AC: 602 AN: 10632

Ashkenazi Jewish (ASJ) AF: 0.0708 AC: 236 AN: 3334

East Asian (EAS) AF: 0.00126 AC: 5 AN: 3982

South Asian (SAS) AF: 0.0405 AC: 153 AN: 3780

European-Finnish (FIN) AF: 0.0487 AC: 282 AN: 5788

Middle Eastern (MID) AF: 0.119 AC: 26 AN: 218

European-Non Finnish (NFE) AF: 0.0632 AC: 4005 AN: 63366

Other (OTH) AF: 0.0779 AC: 135 AN: 1732

Alfa AF: 0.0584 Hom.: 40

Bravo AF: 0.0711

Asia WGS AF: 0.0280 AC: 97 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2529080; hg19: chr7-24558287;