14-65308977-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553754.1(ENSG00000258760):n.300+9514A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,914 control chromosomes in the GnomAD database, including 15,062 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 0.43 (15062 hom., cov: 31)
• Consequence: ENST00000553754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000553754.1	n.300+9514A>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65733 AN: 151796 Hom.: 15041 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.433 AC: 65801 AN: 151914 Hom.: 15062 Cov.: 31 AF XY: 0.444 AC XY: 32953 AN XY: 74220

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.455

Alfa AF: 0.369 Hom.: 13925

Bravo AF: 0.434

Asia WGS AF: 0.662 AC: 2303 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	2.9
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11847263; hg19: chr14-65775695;