5-163617908-A-G

Variant names:

• chr5-163617908-A-G
• rs292411

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 0.448 in 133,300 control chromosomes in the GnomAD database, including 13,369 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 0.45 (13369 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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: 0.448 AC: 59688 AN: 133224 Hom.: 13370 Cov.: 23

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.448 AC: 59700 AN: 133300 Hom.: 13369 Cov.: 23 AF XY: 0.449 AC XY: 28979 AN XY: 64608

African (AFR) AF: 0.337 AC: 10846 AN: 32214

American (AMR) AF: 0.529 AC: 7310 AN: 13824

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1497 AN: 3288

East Asian (EAS) AF: 0.817 AC: 3856 AN: 4718

South Asian (SAS) AF: 0.506 AC: 2154 AN: 4258

European-Finnish (FIN) AF: 0.376 AC: 3123 AN: 8304

Middle Eastern (MID) AF: 0.485 AC: 127 AN: 262

European-Non Finnish (NFE) AF: 0.463 AC: 29465 AN: 63704

Other (OTH) AF: 0.460 AC: 869 AN: 1890

Alfa AF: 0.406 Hom.: 1614

Bravo AF: 0.423

Asia WGS AF: 0.588 AC: 2043 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs292411; hg19: chr5-163044914;