7-155088459-G-T

Variant names:

• chr7-155088459-G-T
• rs1657273

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 0.284 in 151,272 control chromosomes in the GnomAD database, including 6,512 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 0.28 (6512 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.285 AC: 43006 AN: 151156 Hom.: 6509 Cov.: 30

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.284 AC: 43016 AN: 151272 Hom.: 6512 Cov.: 30 AF XY: 0.287 AC XY: 21196 AN XY: 73890

African (AFR) AF: 0.207 AC: 8550 AN: 41242

American (AMR) AF: 0.294 AC: 4485 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 896 AN: 3460

East Asian (EAS) AF: 0.528 AC: 2709 AN: 5126

South Asian (SAS) AF: 0.342 AC: 1637 AN: 4780

European-Finnish (FIN) AF: 0.313 AC: 3253 AN: 10408

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20449 AN: 67726

Other (OTH) AF: 0.286 AC: 599 AN: 2096

Alfa AF: 0.293 Hom.: 22602

Bravo AF: 0.286

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.78
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1657273; hg19: chr7-154880169;