7-24133347-T-C

Variant names:

• chr7-24133347-T-C
• rs1978145

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;