rs12655062

Positions:

• chr5-1890763-G-A
• chr5-1890763-G-C
• chr5-1890763-G-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.109+2481G>A 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 0.304 in 152,140 control chromosomes in the GnomAD database, including 7,835 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 0.30 (7835 hom., cov: 33)
• Consequence: CTD-2194D22.4 NR_109912.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTD-2194D22.4	NR_109912.1	n.109+2481G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTD-2194D22.4	ENST00000514569.1	n.108+2481G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46250 AN: 152022 Hom.: 7825 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.304 AC: 46280 AN: 152140 Hom.: 7835 Cov.: 33 AF XY: 0.314 AC XY: 23340 AN XY: 74368

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.342

Alfa AF: 0.289 Hom.: 2189

Bravo AF: 0.296

Asia WGS AF: 0.364 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
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: rs12655062; hg19: chr5-1890877;