16-62128992-A-T

Variant summary

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

The XR_007065218.1(LOC124903778):n.165-649A>T 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 0.836 in 152,182 control chromosomes in the GnomAD database, including 53,483 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 0.84 (53483 hom., cov: 32)
• Consequence: LOC124903778 XR_007065218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727

Genes affected

LOC124903778 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903778	XR_007065218.1	n.165-649A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127131 AN: 152064 Hom.: 53449 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.836 AC: 127220 AN: 152182 Hom.: 53483 Cov.: 32 AF XY: 0.842 AC XY: 62654 AN XY: 74398

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.828

Alfa AF: 0.765 Hom.: 2607

Bravo AF: 0.835

Asia WGS AF: 0.950 AC: 3304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	5.2
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8045513; hg19: chr16-62162896;