22-46143761-C-T

Position:

• chr22-46143761-C-T

Variant summary

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

The XR_007068140.1(LOC124905138):​n.468G>A 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 0.356 in 152,154 control chromosomes in the GnomAD database, including 11,920 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 0.36 (11920 hom., cov: 33)
• Consequence: LOC124905138 XR_007068140.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

Genes affected

LOC124905138 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=15.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905138	XR_007068140.1	n.468G>A		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54144 AN: 152036 Hom.: 11892 Cov.: 33

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0808

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.356 AC: 54222 AN: 152154 Hom.: 11920 Cov.: 33 AF XY: 0.347 AC XY: 25852 AN XY: 74402

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0808

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.323

Alfa AF: 0.350 Hom.: 2043

Bravo AF: 0.367

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs135562; hg19: -;