ENST00000846025.1:n.288+508T>C

Variant names:

• chr16-19933041-A-G
• rs11639988
• ENST00000846025.1:n.288+508T>C

Variant summary

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

The ENST00000846025.1(ENSG00000309935):​n.288+508T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 151,984 control chromosomes in the GnomAD database, including 2,136 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 0.16 (2136 hom., cov: 31)
• Consequence: ENSG00000309935 ENST00000846025.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 24 publications found

Genes affected

ENSG00000309935 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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
ENSG00000309935	ENST00000846025.1	n.288+508T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23565 AN: 151866 Hom.: 2142 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.155 AC: 23584 AN: 151984 Hom.: 2136 Cov.: 31 AF XY: 0.150 AC XY: 11134 AN XY: 74288

African (AFR) AF: 0.238 AC: 9873 AN: 41398

American (AMR) AF: 0.108 AC: 1655 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5164

South Asian (SAS) AF: 0.0440 AC: 212 AN: 4814

European-Finnish (FIN) AF: 0.117 AC: 1241 AN: 10578

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9640 AN: 67964

Other (OTH) AF: 0.139 AC: 294 AN: 2114

Alfa AF: 0.146 Hom.: 3345

Bravo AF: 0.160

Asia WGS AF: 0.0450 AC: 160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.74
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs11639988; hg19: chr16-19944363;