14-94546047-A-G

Variant summary

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

The ENST00000658195.1(ENSG00000287668):n.149-211A>G 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 0.619 in 152,168 control chromosomes in the GnomAD database, including 29,553 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 0.62 (29553 hom., cov: 34)
• Consequence: ENST00000658195.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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
	ENST00000658195.1	n.149-211A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94060 AN: 152050 Hom.: 29530 Cov.: 34

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.619 AC: 94131 AN: 152168 Hom.: 29553 Cov.: 34 AF XY: 0.621 AC XY: 46234 AN XY: 74398

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.613

Alfa AF: 0.571 Hom.: 23236

Bravo AF: 0.613

Asia WGS AF: 0.743 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.30
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11160190; hg19: chr14-95012384;