rs919334

Variant names:

• chr5-111217704-A-G
• rs919334

Your query was ambiguous. Multiple possible variants found:

• chr5-111217704-A-G
• chr5-111217704-A-T

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 0.381 in 151,794 control chromosomes in the GnomAD database, including 11,296 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 0.38 (11296 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57841 AN: 151676 Hom.: 11298 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.381 AC: 57864 AN: 151794 Hom.: 11296 Cov.: 31 AF XY: 0.383 AC XY: 28432 AN XY: 74174

African (AFR) AF: 0.458 AC: 18955 AN: 41388

American (AMR) AF: 0.371 AC: 5652 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1088 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5160

South Asian (SAS) AF: 0.460 AC: 2217 AN: 4820

European-Finnish (FIN) AF: 0.370 AC: 3895 AN: 10528

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23909 AN: 67866

Other (OTH) AF: 0.358 AC: 753 AN: 2106

Alfa AF: 0.352 Hom.: 17879

Bravo AF: 0.379

Asia WGS AF: 0.330 AC: 1146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.97
DANN	Benign	0.68
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs919334; hg19: chr5-110553402;