rs7187476

chr16-67666045-T-C

Variant summary

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

The NM_032140.3(ENKD1):c.280+26A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,605,300 control chromosomes in the GnomAD database, including 36,489 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 (10208 hom., cov: 33)
  • Exomes 𝑓: 0.17 (26281 hom.)
• Consequence: ENKD1 NM_032140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

Genes affected

ENKD1 (HGNC:25246): (enkurin domain containing 1) Located in cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]

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 (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENKD1	NM_032140.3	c.280+26A>G		intron_variant		ENST00000243878.9
ENKD1	XM_024450469.2	c.280+26A>G		intron_variant
ENKD1	XM_024450470.2	c.280+26A>G		intron_variant
ENKD1	NR_138150.2	n.588+26A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENKD1	ENST00000243878.9	c.280+26A>G		intron_variant		1	NM_032140.3	P1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45069 AN: 152050 Hom.: 10172 Cov.: 33

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.264

GnomAD3 exomes AF: 0.198 AC: 47794 AN: 240986 Hom.: 6804 AF XY: 0.192 AC XY: 25386 AN XY: 131966

Gnomad AFR exome AF: 0.640

Gnomad AMR exome AF: 0.197

Gnomad ASJ exome AF: 0.157

Gnomad EAS exome AF: 0.0243

Gnomad SAS exome AF: 0.255

Gnomad FIN exome AF: 0.180

Gnomad NFE exome AF: 0.159

Gnomad OTH exome AF: 0.186

GnomAD4 exome AF: 0.169 AC: 246251 AN: 1453132 Hom.: 26281 Cov.: 32 AF XY: 0.171 AC XY: 123241 AN XY: 722212

Gnomad4 AFR exome AF: 0.652

Gnomad4 AMR exome AF: 0.204

Gnomad4 ASJ exome AF: 0.163

Gnomad4 EAS exome AF: 0.0341

Gnomad4 SAS exome AF: 0.244

Gnomad4 FIN exome AF: 0.180

Gnomad4 NFE exome AF: 0.151

Gnomad4 OTH exome AF: 0.189

GnomAD4 genome AF: 0.297 AC: 45156 AN: 152168 Hom.: 10208 Cov.: 33 AF XY: 0.294 AC XY: 21878 AN XY: 74382

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0295

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.265

Alfa AF: 0.182 Hom.: 2633

Bravo AF: 0.310

Asia WGS AF: 0.214 AC: 746 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	4.7
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7187476; hg19: chr16-67699948; COSMIC: COSV54677622; COSMIC: COSV54677622;