rs6997249

Positions:

• chr8-129484119-G-A

Variant summary

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

The NR_037457.1(MIR3686):​n.24C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 154,620 control chromosomes in the GnomAD database, including 6,402 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 0.28 (6295 hom., cov: 32)
  • Exomes 𝑓: 0.28 (107 hom.)
• Consequence: MIR3686 NR_037457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

CCDC26 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3686	NR_037457.1	n.24C>T		non_coding_transcript_exon_variant	1/1
CCDC26	NR_130917.1	n.313-3429C>T		intron_variant
CCDC26	NR_130918.1	n.137+90763C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.313-3429C>T		intron_variant		1
CCDC26	ENST00000523151.6	n.135+90763C>T		intron_variant		1
MIR3686	ENST00000577904.1	n.24C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42090 AN: 151980 Hom.: 6293 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.269

GnomAD3 exomes AF: 0.298 AC: 1583 AN: 5318 Hom.: 228 AF XY: 0.315 AC XY: 791 AN XY: 2508

Gnomad AFR exome AF: 0.217

Gnomad AMR exome AF: 0.264

Gnomad ASJ exome AF: 0.327

Gnomad EAS exome AF: 0.0469

Gnomad SAS exome AF: 0.173

Gnomad NFE exome AF: 0.312

Gnomad OTH exome AF: 0.218

GnomAD4 exome AF: 0.280 AC: 707 AN: 2522 Hom.: 107 Cov.: 0 AF XY: 0.298 AC XY: 391 AN XY: 1310

Gnomad4 AFR exome AF: 0.237

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.208

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.287

Gnomad4 OTH exome AF: 0.253

GnomAD4 genome AF: 0.277 AC: 42103 AN: 152098 Hom.: 6295 Cov.: 32 AF XY: 0.279 AC XY: 20775 AN XY: 74354

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.268

Alfa AF: 0.317 Hom.: 988

Bravo AF: 0.266

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6997249; hg19: chr8-130496365;