rs3136038

chr16-13919522-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124903647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124903647	XR_007065001.1	n.462G>A		non_coding_transcript_exon_variant	2/2
LOC105371093	XR_007065000.1	n.82+7003G>A		intron_variant, non_coding_transcript_variant
LOC105371093	XR_007064999.1	n.82+7003G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.366

Alfa AF: 0.368 Hom.: 1857

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3136038; hg19: chr16-14013379;