7-155093375-T-C

Position:

• chr7-155093375-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 0.704 in 152,114 control chromosomes in the GnomAD database, including 38,607 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 0.70 (38607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106974 AN: 151996 Hom.: 38565 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.704 AC: 107064 AN: 152114 Hom.: 38607 Cov.: 32 AF XY: 0.700 AC XY: 52041 AN XY: 74366

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.681

Alfa AF: 0.673 Hom.: 4375

Bravo AF: 0.717

Asia WGS AF: 0.596 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1730135; hg19: chr7-154885085;