ENST00000770016.1:n.369+14910C>T

Variant names:

• chr14-54373178-G-A
• rs1950202
• ENST00000770016.1:n.369+14910C>T

Variant summary

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

The ENST00000770016.1(ENSG00000300202):​n.369+14910C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 148,614 control chromosomes in the GnomAD database, including 9,545 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 0.35 (9545 hom., cov: 27)
• Consequence: ENSG00000300202 ENST00000770016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 6 publications found

Genes affected

ENSG00000300202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 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
ENSG00000300202	ENST00000770016.1	n.369+14910C>T		intron_variant	Intron 3 of 3
ENSG00000300202	ENST00000770017.1	n.409+14910C>T		intron_variant	Intron 2 of 2
ENSG00000300202	ENST00000770018.1	n.521+3463C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.351 AC: 52185 AN: 148498 Hom.: 9543 Cov.: 27

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.393

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.351 AC: 52224 AN: 148614 Hom.: 9545 Cov.: 27 AF XY: 0.350 AC XY: 25277 AN XY: 72300

African (AFR) AF: 0.456 AC: 18531 AN: 40642

American (AMR) AF: 0.275 AC: 4055 AN: 14746

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1008 AN: 3444

East Asian (EAS) AF: 0.402 AC: 2048 AN: 5100

South Asian (SAS) AF: 0.482 AC: 2276 AN: 4720

European-Finnish (FIN) AF: 0.241 AC: 2352 AN: 9774

Middle Eastern (MID) AF: 0.398 AC: 113 AN: 284

European-Non Finnish (NFE) AF: 0.310 AC: 20788 AN: 66992

Other (OTH) AF: 0.351 AC: 712 AN: 2026

Alfa AF: 0.322 Hom.: 15866

Bravo AF: 0.349

Asia WGS AF: 0.432 AC: 1496 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.8
DANN	Benign	0.75
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1950202; hg19: chr14-54839896;