rs72766477

Variant names:

• chr5-84611411-G-A
• rs72766477

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0312 in 151,792 control chromosomes in the GnomAD database, including 169 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 0.031 (169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0312 (4731/151792) while in subpopulation NFE AF = 0.0387 (2627/67924). AF 95% confidence interval is 0.0374. There are 169 homozygotes in GnomAd4. There are 2462 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 169 gene

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: 0.0312 AC: 4731 AN: 151678 Hom.: 168 Cov.: 32

Gnomad AFR AF: 0.00530

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0176

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0312 AC: 4731 AN: 151792 Hom.: 169 Cov.: 32 AF XY: 0.0332 AC XY: 2462 AN XY: 74192

African (AFR) AF: 0.00529 AC: 219 AN: 41410

American (AMR) AF: 0.0175 AC: 267 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3468

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5156

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4814

European-Finnish (FIN) AF: 0.120 AC: 1258 AN: 10486

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0387 AC: 2627 AN: 67924

Other (OTH) AF: 0.0237 AC: 50 AN: 2108

Alfa AF: 0.0352 Hom.: 110

Bravo AF: 0.0220

Asia WGS AF: 0.0110 AC: 38 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.21
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs72766477; hg19: chr5-83907229;