7-155093375-T-C

Variant names:

• chr7-155093375-T-C
• rs1730135

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;