rs35679096

Positions:

• chr22-28804405-G-A
• chr22-28804405-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000458080.1(ENSG00000226471):​n.55+3668G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.021 in 151,886 control chromosomes in the GnomAD database, including 53 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 0.021 (53 hom., cov: 30)
• Consequence: ENST00000458080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.021 (3190/151886) while in subpopulation NFE AF= 0.0334 (2270/67950). AF 95% confidence interval is 0.0323. There are 53 homozygotes in gnomad4. There are 1453 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 53 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000458080.1	n.55+3668G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0210 AC: 3190 AN: 151770 Hom.: 53 Cov.: 30

Gnomad AFR AF: 0.00584

Gnomad AMI AF: 0.0573

Gnomad AMR AF: 0.0125

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0221

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

GnomAD4 genome AF: 0.0210 AC: 3190 AN: 151886 Hom.: 53 Cov.: 30 AF XY: 0.0196 AC XY: 1453 AN XY: 74236

Gnomad4 AFR AF: 0.00582

Gnomad4 AMR AF: 0.0125

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0334

Gnomad4 OTH AF: 0.0219

Alfa AF: 0.0191 Hom.: 8

Bravo AF: 0.0192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
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: rs35679096; hg19: chr22-29200393;