rs3136038

Variant names:

• chr16-13919522-C-T
• rs3136038
• XR_007065001.1:n.462G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065001.1(LOC124903647):​n.462G>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 0.36 in 151,638 control chromosomes in the GnomAD database, including 10,324 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 0.36 (10324 hom., cov: 31)
• Consequence: LOC124903647 XR_007065001.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 21 publications found

Genes affected

LOC124903647 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54461 AN: 151520 Hom.: 10297 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.360 AC: 54537 AN: 151638 Hom.: 10324 Cov.: 31 AF XY: 0.355 AC XY: 26325 AN XY: 74092

African (AFR) AF: 0.469 AC: 19389 AN: 41302

American (AMR) AF: 0.278 AC: 4238 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1348 AN: 5142

South Asian (SAS) AF: 0.271 AC: 1297 AN: 4792

European-Finnish (FIN) AF: 0.305 AC: 3194 AN: 10468

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.332 AC: 22524 AN: 67920

Other (OTH) AF: 0.366 AC: 769 AN: 2100

Alfa AF: 0.371 Hom.: 1942

Bravo AF: 0.363

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs3136038; hg19: chr16-14013379;