7-152638744-A-G

Position:

• chr7-152638744-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;