14-20414432-T-C

Variant names:

• chr14-20414432-T-C
• rs4246977
• ENST00000773014.1:n.660T>C

Variant summary

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

The ENST00000773014.1(ENSG00000300624):​n.660T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,068 control chromosomes in the GnomAD database, including 9,971 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 0.36 (9971 hom., cov: 32)
• Consequence: ENSG00000300624 ENST00000773014.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 10 publications found

Genes affected

ENSG00000300624 (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 (SAS) allele frequency at 95% confidence interval = 0.429 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
ENSG00000300624	ENST00000773014.1	n.660T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000300624	ENST00000773015.1	n.931T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54482 AN: 151952 Hom.: 9955 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.359 AC: 54538 AN: 152068 Hom.: 9971 Cov.: 32 AF XY: 0.360 AC XY: 26784 AN XY: 74360

African (AFR) AF: 0.298 AC: 12361 AN: 41456

American (AMR) AF: 0.329 AC: 5031 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3466

East Asian (EAS) AF: 0.306 AC: 1582 AN: 5168

South Asian (SAS) AF: 0.445 AC: 2143 AN: 4820

European-Finnish (FIN) AF: 0.379 AC: 4014 AN: 10584

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26864 AN: 67966

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.382 Hom.: 43934

Bravo AF: 0.349

Asia WGS AF: 0.319 AC: 1109 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	4.2
DANN	Benign	0.59
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs4246977; hg19: chr14-20882591;