ENST00000777615.1:n.93-17895T>C

Variant names:

• chr14-92851221-A-G
• rs11622505
• ENST00000777615.1:n.93-17895T>C

Variant summary

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

The ENST00000777615.1(ENSG00000301280):​n.93-17895T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,114 control chromosomes in the GnomAD database, including 1,765 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 0.13 (1765 hom., cov: 31)
• Consequence: ENSG00000301280 ENST00000777615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 4 publications found

Genes affected

ENSG00000301280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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
ENSG00000301280	ENST00000777615.1	n.93-17895T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20464 AN: 151996 Hom.: 1765 Cov.: 31

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.135 AC: 20462 AN: 152114 Hom.: 1765 Cov.: 31 AF XY: 0.128 AC XY: 9526 AN XY: 74360

African (AFR) AF: 0.0504 AC: 2095 AN: 41552

American (AMR) AF: 0.112 AC: 1717 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3470

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5178

South Asian (SAS) AF: 0.0994 AC: 478 AN: 4810

European-Finnish (FIN) AF: 0.124 AC: 1308 AN: 10578

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13580 AN: 67936

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.161 Hom.: 661

Bravo AF: 0.132

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.85
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11622505; hg19: chr14-93317566;