chr16-13919522-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903647	XR_007065001.1	n.462G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105371093	XR_007064999.1	n.82+7003G>A		intron_variant	Intron 1 of 2
LOC105371093	XR_007065000.1	n.82+7003G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;