16-49404129-A-G

Position:

• chr16-49404129-A-G

Variant summary

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

The XR_001752167.2(LOC105371244):​n.1812+5220T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,742 control chromosomes in the GnomAD database, including 18,498 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 0.46 (18498 hom., cov: 30)
• Consequence: LOC105371244 XR_001752167.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

LOC105371244 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371244	XR_001752167.2	n.1812+5220T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69234 AN: 151622 Hom.: 18468 Cov.: 30

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.457 AC: 69312 AN: 151742 Hom.: 18498 Cov.: 30 AF XY: 0.452 AC XY: 33479 AN XY: 74116

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.421

Alfa AF: 0.381 Hom.: 6088

Bravo AF: 0.462

Asia WGS AF: 0.472 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs27807; hg19: chr16-49438040;