5-1895715-C-T

Position:

• chr5-1895715-C-T

Variant summary

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

The NR_109912.1(CTD-2194D22.4):​n.110-2330C>T 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 0.428 in 151,972 control chromosomes in the GnomAD database, including 14,072 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 (14072 hom., cov: 33)
• Consequence: CTD-2194D22.4 NR_109912.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

CTD-2194D22.4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTD-2194D22.4	NR_109912.1	n.110-2330C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTD-2194D22.4	ENST00000514569.1	n.109-2330C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64962 AN: 151854 Hom.: 14047 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.428 AC: 65042 AN: 151972 Hom.: 14072 Cov.: 33 AF XY: 0.433 AC XY: 32169 AN XY: 74274

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.443

Alfa AF: 0.430 Hom.: 32766

Bravo AF: 0.428

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12653946; hg19: chr5-1895829;