16-85977427-C-T

Variant summary

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

The XR_007065161.1(LOC124903741):n.7682G>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 0.237 in 152,080 control chromosomes in the GnomAD database, including 4,741 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 0.24 (4741 hom., cov: 33)
• Consequence: LOC124903741 XR_007065161.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

LOC124903741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903741	XR_007065161.1	n.7682G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000645754.1	n.227+7015G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36048 AN: 151962 Hom.: 4727 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.237 AC: 36093 AN: 152080 Hom.: 4741 Cov.: 33 AF XY: 0.238 AC XY: 17685 AN XY: 74334

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.237

Alfa AF: 0.209 Hom.: 3997

Bravo AF: 0.261

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13333054; hg19: chr16-86011033;