rs893109

Positions:

• chr7-155101164-G-A
• chr7-155101164-G-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 0.283 in 152,124 control chromosomes in the GnomAD database, including 6,480 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 (6480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 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: 0.284 AC: 43109 AN: 152006 Hom.: 6476 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.283 AC: 43121 AN: 152124 Hom.: 6480 Cov.: 33 AF XY: 0.286 AC XY: 21284 AN XY: 74398

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.281

Alfa AF: 0.290 Hom.: 3268

Bravo AF: 0.284

Asia WGS AF: 0.389 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs893109; hg19: chr7-154892874;