rs899729

Variant names:

• chr16-88635372-C-A
• rs899729
• XR_007065181.1:n.365C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

LOC124903755 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.514 AC: 21328 AN: 41468

American (AMR) AF: 0.291 AC: 4454 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.120 AC: 622 AN: 5174

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4828

European-Finnish (FIN) AF: 0.408 AC: 4317 AN: 10592

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27661 AN: 67956

Other (OTH) AF: 0.350 AC: 740 AN: 2114

Alfa AF: 0.395 Hom.: 38806

Bravo AF: 0.400

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.0
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs899729; hg19: chr16-88701780;