5-56408415-G-T

Variant names:

• chr5-56408415-G-T
• rs11741905

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 0.224 in 152,048 control chromosomes in the GnomAD database, including 4,298 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 0.22 (4298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.308 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: 0.224 AC: 34098 AN: 151928 Hom.: 4288 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.224 AC: 34112 AN: 152048 Hom.: 4298 Cov.: 32 AF XY: 0.224 AC XY: 16671 AN XY: 74324

African (AFR) AF: 0.121 AC: 5035 AN: 41468

American (AMR) AF: 0.316 AC: 4823 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1599 AN: 5174

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4808

European-Finnish (FIN) AF: 0.269 AC: 2843 AN: 10552

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17314 AN: 67984

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.251 Hom.: 3006

Bravo AF: 0.227

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.3
DANN	Benign	0.64
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs11741905; hg19: chr5-55704242;