rs162307

Variant names:

• chr5-119747260-A-G
• rs162307

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 0.849 in 152,238 control chromosomes in the GnomAD database, including 55,615 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 0.85 (55615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• 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 = 0.955 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: 0.849 AC: 129214 AN: 152120 Hom.: 55562 Cov.: 32

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.849 AC: 129319 AN: 152238 Hom.: 55615 Cov.: 32 AF XY: 0.842 AC XY: 62670 AN XY: 74410

African (AFR) AF: 0.963 AC: 40025 AN: 41554

American (AMR) AF: 0.707 AC: 10816 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3243 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3605 AN: 5176

South Asian (SAS) AF: 0.823 AC: 3963 AN: 4818

European-Finnish (FIN) AF: 0.790 AC: 8370 AN: 10594

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56300 AN: 68006

Other (OTH) AF: 0.882 AC: 1866 AN: 2116

Alfa AF: 0.833 Hom.: 31157

Bravo AF: 0.847

Asia WGS AF: 0.718 AC: 2496 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	0.98
DANN	Benign	0.69
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs162307; hg19: chr5-119082955;