rs755775

Variant names:

• chr5-100645361-A-G
• rs755775

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 0.127 in 152,230 control chromosomes in the GnomAD database, including 2,406 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 0.13 (2406 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.127 AC: 19252 AN: 152112 Hom.: 2394 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.0888

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

GnomAD4 genome AF: 0.127 AC: 19295 AN: 152230 Hom.: 2406 Cov.: 33 AF XY: 0.123 AC XY: 9179 AN XY: 74438

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.0497

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0420

Gnomad4 FIN AF: 0.0900

Gnomad4 NFE AF: 0.0512

Gnomad4 OTH AF: 0.0879

Alfa AF: 0.0820 Hom.: 239

Bravo AF: 0.133

Asia WGS AF: 0.0340 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs755775; hg19: chr5-99981065;