7-152638744-A-G

Variant names:

• chr7-152638744-A-G
• rs718282

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 0.938 in 151,376 control chromosomes in the GnomAD database, including 66,691 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 0.94 (66691 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.939 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: 0.938 AC: 141937 AN: 151258 Hom.: 66636 Cov.: 26

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.938 AC: 142048 AN: 151376 Hom.: 66691 Cov.: 26 AF XY: 0.940 AC XY: 69430 AN XY: 73892

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.928

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.927

Alfa AF: 0.940 Hom.: 8342

Bravo AF: 0.933

Asia WGS AF: 0.908 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718282; hg19: chr7-152335829;