rs17445836

Positions:

• chr16-85984057-G-A

Variant summary

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

The XR_007065161.1(LOC124903741):​n.1052C>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 0.152 in 152,082 control chromosomes in the GnomAD database, including 2,388 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 0.15 (2388 hom., cov: 33)
• Consequence: LOC124903741 XR_007065161.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

LOC124903741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903741	XR_007065161.1	n.1052C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000599411.2	n.123-315G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000645754.1	n.227+385C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23089 AN: 151966 Hom.: 2385 Cov.: 33

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0662

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.152 AC: 23113 AN: 152082 Hom.: 2388 Cov.: 33 AF XY: 0.152 AC XY: 11325 AN XY: 74348

Gnomad4 AFR AF: 0.0442

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0663

Gnomad4 SAS AF: 0.0828

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.136

Alfa AF: 0.208 Hom.: 1890

Bravo AF: 0.131

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17445836; hg19: chr16-86017663;