22-28846485-T-C

Position:

• chr22-28846485-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002958745.2(LOC107985549):​n.1531T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,126 control chromosomes in the GnomAD database, including 1,927 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 0.14 (1927 hom., cov: 32)
• Consequence: LOC107985549 XR_002958745.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630

Genes affected

LOC107985549 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985549	XR_002958745.2	n.1531T>C		non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000458080.1	n.337-1906T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21150 AN: 152008 Hom.: 1927 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.139 AC: 21156 AN: 152126 Hom.: 1927 Cov.: 32 AF XY: 0.145 AC XY: 10757 AN XY: 74374

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.172

Alfa AF: 0.0681 Hom.: 113

Bravo AF: 0.126

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.3
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5762852; hg19: chr22-29242473;