16-11527267-C-T

Variant names:

• chr16-11527267-C-T
• rs4131547
• XM_047434105.1:c.-92G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

LOC400499 (HGNC:):

LOC400499 (HGNC:0):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC400499	XM_047434105.1	c.-92G>A		5_prime_UTR_variant	Exon 1 of 67		XP_047290061.1
LOC400499	NM_001370704.1	c.-92G>A		upstream_gene_variant		ENST00000696174.1	NP_001357633.1
LOC400499	NM_001395505.1	c.-92G>A		upstream_gene_variant			NP_001382434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000188897	ENST00000696174.1	c.-92G>A		upstream_gene_variant			NM_001370704.1	ENSP00000512464.1
ENSG00000188897	ENST00000598234.6	c.-92G>A		upstream_gene_variant		5		ENSP00000470478.3

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

African (AFR) AF: 0.334 AC: 13811 AN: 41410

American (AMR) AF: 0.126 AC: 1932 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5170

South Asian (SAS) AF: 0.0872 AC: 420 AN: 4816

European-Finnish (FIN) AF: 0.166 AC: 1759 AN: 10586

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12776 AN: 67968

Other (OTH) AF: 0.171 AC: 361 AN: 2108

Alfa AF: 0.184 Hom.: 1060

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
PhyloP100		-0.45
PromoterAI		-0.0073	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4131547; hg19: chr16-11621123;