rs755775

Variant names:

• chr5-100645361-A-G
• rs755775

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 0.127 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.324 AC: 13447 AN: 41488

American (AMR) AF: 0.0497 AC: 760 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5194

South Asian (SAS) AF: 0.0420 AC: 203 AN: 4832

European-Finnish (FIN) AF: 0.0900 AC: 955 AN: 10606

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0512 AC: 3482 AN: 68018

Other (OTH) AF: 0.0879 AC: 186 AN: 2116

Alfa AF: 0.0864 Hom.: 276

Bravo AF: 0.133

Asia WGS AF: 0.0340 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.56
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs755775; hg19: chr5-99981065;