16-11527267-C-T

Position:

• chr16-11527267-C-T

Variant summary

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

The XM_047434105.1(LOC400499):​c.-92G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,030 control chromosomes in the GnomAD database, including 3,779 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 0.21 (3779 hom., cov: 32)
• Consequence: LOC400499 XM_047434105.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

Genes affected

LOC400499 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC400499	XM_047434105.1	c.-92G>A		5_prime_UTR_variant	1/67		XP_047290061.1
LOC400499	NM_001370704.1			upstream_gene_variant		ENST00000696174.1	NP_001357633.1
LOC400499	NM_001395505.1			upstream_gene_variant			NP_001382434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000696174.1			upstream_gene_variant			NM_001370704.1	ENSP00000512464	A2
	ENST00000598234.6			upstream_gene_variant		5		ENSP00000470478	P4

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31827 AN: 151912 Hom.: 3767 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.210 AC: 31868 AN: 152030 Hom.: 3779 Cov.: 32 AF XY: 0.205 AC XY: 15210 AN XY: 74338

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0872

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.171

Alfa AF: 0.192 Hom.: 588

Bravo AF: 0.213

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131547; hg19: chr16-11621123;