5-109613236-C-T

Variant names:

• chr5-109613236-C-T
• rs367615

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 0.779 in 151,544 control chromosomes in the GnomAD database, including 46,622 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 0.78 (46622 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.779 AC: 117914 AN: 151424 Hom.: 46582 Cov.: 27

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.779 AC: 118008 AN: 151544 Hom.: 46622 Cov.: 27 AF XY: 0.764 AC XY: 56535 AN XY: 73976

African (AFR) AF: 0.840 AC: 34725 AN: 41360

American (AMR) AF: 0.664 AC: 10099 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2733 AN: 3464

East Asian (EAS) AF: 0.471 AC: 2344 AN: 4978

South Asian (SAS) AF: 0.722 AC: 3459 AN: 4794

European-Finnish (FIN) AF: 0.659 AC: 6930 AN: 10520

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.814 AC: 55308 AN: 67906

Other (OTH) AF: 0.774 AC: 1629 AN: 2106

Alfa AF: 0.796 Hom.: 112916

Bravo AF: 0.778

Asia WGS AF: 0.574 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.014
DANN	Benign	0.52
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs367615; hg19: chr5-108948937;