rs16949856

Variant names:

• chr15-45980660-C-T
• rs16949856
• ENST00000773915.1:n.111+31472C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000773915.1(ENSG00000300769):​n.111+31472C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,006 control chromosomes in the GnomAD database, including 4,354 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 0.23 (4354 hom., cov: 32)
• Consequence: ENSG00000300769 ENST00000773915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 1 publications found

Genes affected

ENSG00000300769 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300769	ENST00000773915.1	n.111+31472C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35301 AN: 151888 Hom.: 4348 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.00908

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.232 AC: 35317 AN: 152006 Hom.: 4354 Cov.: 32 AF XY: 0.230 AC XY: 17095 AN XY: 74300

African (AFR) AF: 0.256 AC: 10613 AN: 41458

American (AMR) AF: 0.173 AC: 2634 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3470

East Asian (EAS) AF: 0.00891 AC: 46 AN: 5164

South Asian (SAS) AF: 0.119 AC: 572 AN: 4824

European-Finnish (FIN) AF: 0.278 AC: 2932 AN: 10558

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16992 AN: 67954

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.251 Hom.: 653

Bravo AF: 0.223

Asia WGS AF: 0.0780 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs16949856; hg19: chr15-46272858;