16-1943476-A-G

Position:

• chr16-1943476-A-G

Variant summary

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

The XR_007064940.1(LOC124903625):​n.580A>G 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 0.533 in 379,058 control chromosomes in the GnomAD database, including 59,731 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 0.58 (28400 hom., cov: 32)
  • Exomes 𝑓: 0.50 (31331 hom.)
• Consequence: LOC124903625 XR_007064940.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

LOC124903625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903625	XR_007064940.1	n.580A>G		non_coding_transcript_exon_variant	2/2
		n.1943476A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88168 AN: 151804 Hom.: 28341 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.539

GnomAD4 exome AF: 0.501 AC: 113761 AN: 227138 Hom.: 31331 AF XY: 0.525 AC XY: 64069 AN XY: 122028

Gnomad4 AFR exome AF: 0.854

Gnomad4 AMR exome AF: 0.427

Gnomad4 ASJ exome AF: 0.521

Gnomad4 EAS exome AF: 0.669

Gnomad4 SAS exome AF: 0.775

Gnomad4 FIN exome AF: 0.443

Gnomad4 NFE exome AF: 0.416

Gnomad4 OTH exome AF: 0.483

GnomAD4 genome AF: 0.581 AC: 88279 AN: 151920 Hom.: 28400 Cov.: 32 AF XY: 0.587 AC XY: 43603 AN XY: 74252

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.544

Alfa AF: 0.512 Hom.: 3710

Bravo AF: 0.582

Asia WGS AF: 0.727 AC: 2528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs732510; hg19: chr16-1993477;