15-25120022-CACAG-C

Position:

• chr15-25120022-CACAG-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000626200.3(SNHG14):​n.1347_1350delGACA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.52 (21750 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: SNHG14 ENST00000626200.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

SNHG14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IPW	NR_023915.1	n.2048_2051delGACA		non_coding_transcript_exon_variant	3/3
SNHG14	NR_146177.1	n.10396+1644_10396+1647delGACA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG14	ENST00000626200.3	n.1347_1350delGACA		non_coding_transcript_exon_variant	5/5	1
SNHG14	ENST00000549804.7	n.5394_5397delGACA		non_coding_transcript_exon_variant	33/33	5
SNHG14	ENST00000640631.2	n.12668_12671delGACA		non_coding_transcript_exon_variant	38/38	5

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78309 AN: 151472 Hom.: 21757 Cov.: 0

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.517 AC: 78306 AN: 151590 Hom.: 21750 Cov.: 0 AF XY: 0.513 AC XY: 37955 AN XY: 74004

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.518

Alfa AF: 0.564 Hom.: 3071

Bravo AF: 0.500

Asia WGS AF: 0.385 AC: 1339 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16416; hg19: chr15-25365169;