rs72766477

Positions:

• chr5-84611411-G-A

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 169 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84611411G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.00529

Gnomad4 AMR AF: 0.0175

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0395 Hom.: 50

Bravo AF: 0.0220

Asia WGS AF: 0.0110 AC: 38 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72766477; hg19: chr5-83907229;