5-161703039-G-C

Variant names:

• chr5-161703039-G-C
• rs6883758

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 0.786 in 152,002 control chromosomes in the GnomAD database, including 47,242 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 0.79 (47242 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.884 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: 0.786 AC: 119339 AN: 151884 Hom.: 47229 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.786 AC: 119406 AN: 152002 Hom.: 47242 Cov.: 31 AF XY: 0.783 AC XY: 58158 AN XY: 74284

African (AFR) AF: 0.752 AC: 31184 AN: 41468

American (AMR) AF: 0.699 AC: 10669 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2910 AN: 3468

East Asian (EAS) AF: 0.620 AC: 3180 AN: 5126

South Asian (SAS) AF: 0.907 AC: 4374 AN: 4824

European-Finnish (FIN) AF: 0.760 AC: 8032 AN: 10566

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56636 AN: 67968

Other (OTH) AF: 0.784 AC: 1657 AN: 2114

Alfa AF: 0.773 Hom.: 2445

Bravo AF: 0.772

Asia WGS AF: 0.781 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.16
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs6883758; hg19: chr5-161130045; COSMIC: COSV50878823;