7-24133347-T-C

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 0.592 in 152,182 control chromosomes in the GnomAD database, including 28,025 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 0.59 (28025 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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: 0.592 AC: 90019 AN: 152064 Hom.: 27982 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.592 AC: 90110 AN: 152182 Hom.: 28025 Cov.: 33 AF XY: 0.589 AC XY: 43846 AN XY: 74394

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.580

Alfa AF: 0.522 Hom.: 19061

Bravo AF: 0.589

Asia WGS AF: 0.508 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.20
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1978145; hg19: chr7-24172966;