7-155057913-C-T

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 0.55 in 151,928 control chromosomes in the GnomAD database, including 23,930 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 0.55 (23930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 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: 0.550 AC: 83525 AN: 151810 Hom.: 23923 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.550 AC: 83544 AN: 151928 Hom.: 23930 Cov.: 31 AF XY: 0.545 AC XY: 40488 AN XY: 74244

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.563

Alfa AF: 0.581 Hom.: 7701

Bravo AF: 0.550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.0
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440461; hg19: chr7-154849623;