7-155093375-T-C

Variant names:

• chr7-155093375-T-C
• rs1730135

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.877 AC: 36431 AN: 41518

American (AMR) AF: 0.674 AC: 10310 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2249 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3183 AN: 5170

South Asian (SAS) AF: 0.627 AC: 3013 AN: 4806

European-Finnish (FIN) AF: 0.580 AC: 6118 AN: 10548

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43626 AN: 67994

Other (OTH) AF: 0.681 AC: 1438 AN: 2112

Alfa AF: 0.681 Hom.: 4677

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1730135; hg19: chr7-154885085;