rs899729

chr16-88635372-C-A

Variant summary

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

The XR_007065181.1(LOC124903755):n.365C>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 0.406 in 152,098 control chromosomes in the GnomAD database, including 13,298 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 0.41 (13298 hom., cov: 33)
• Consequence: LOC124903755 XR_007065181.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

Genes affected

LOC124903755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903755	XR_007065181.1	n.365C>A		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61639 AN: 151980 Hom.: 13288 Cov.: 33

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.406 AC: 61678 AN: 152098 Hom.: 13298 Cov.: 33 AF XY: 0.398 AC XY: 29576 AN XY: 74340

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.350

Alfa AF: 0.392 Hom.: 15528

Bravo AF: 0.400

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	9.0
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs899729; hg19: chr16-88701780;