22-46143764-G-A

Position:

• chr22-46143764-G-A

Variant summary

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

The XR_007068140.1(LOC124905138):​n.465C>T 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 0.366 in 152,114 control chromosomes in the GnomAD database, including 12,300 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 0.37 (12300 hom., cov: 33)
• Consequence: LOC124905138 XR_007068140.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

Genes affected

LOC124905138 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=14.19).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905138	XR_007068140.1	n.465C>T		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55578 AN: 151996 Hom.: 12272 Cov.: 33

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.366 AC: 55657 AN: 152114 Hom.: 12300 Cov.: 33 AF XY: 0.356 AC XY: 26483 AN XY: 74380

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0810

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.339

Alfa AF: 0.329 Hom.: 1502

Bravo AF: 0.377

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs135561; hg19: -;