5-39861724-T-G

Variant names:

• chr5-39861724-T-G
• rs1816088

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 0.804 in 152,146 control chromosomes in the GnomAD database, including 49,429 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 0.80 (49429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.804 AC: 122239 AN: 152030 Hom.: 49371 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.804 AC: 122354 AN: 152146 Hom.: 49429 Cov.: 32 AF XY: 0.806 AC XY: 59898 AN XY: 74348

African (AFR) AF: 0.877 AC: 36416 AN: 41526

American (AMR) AF: 0.793 AC: 12101 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2418 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4470 AN: 5162

South Asian (SAS) AF: 0.820 AC: 3948 AN: 4816

European-Finnish (FIN) AF: 0.773 AC: 8184 AN: 10594

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52293 AN: 67996

Other (OTH) AF: 0.790 AC: 1666 AN: 2108

Alfa AF: 0.780 Hom.: 171480

Bravo AF: 0.809

Asia WGS AF: 0.859 AC: 2986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.5
DANN	Benign	0.47
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1816088; hg19: chr5-39861826;