rs1853665

Positions:

• chr6-149977706-C-T

Variant summary

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

The ENST00000406262.1(ENSG00000219298):​n.236C>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 0.202 in 850,378 control chromosomes in the GnomAD database, including 21,083 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 0.27 (6700 hom., cov: 33)
  • Exomes 𝑓: 0.19 (14383 hom.)
• Consequence: ENSG00000219298 ENST00000406262.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

ENSG00000219298 (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 (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.149977706C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000219298	ENST00000406262.1	n.236C>T		non_coding_transcript_exon_variant	1/2	6

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40320 AN: 151994 Hom.: 6675 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.259

GnomAD4 exome AF: 0.189 AC: 131808 AN: 698266 Hom.: 14383 Cov.: 9 AF XY: 0.186 AC XY: 69095 AN XY: 372204

Gnomad4 AFR exome AF: 0.455

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.230

Gnomad4 EAS exome AF: 0.376

Gnomad4 SAS exome AF: 0.179

Gnomad4 FIN exome AF: 0.177

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.209

GnomAD4 genome AF: 0.265 AC: 40385 AN: 152112 Hom.: 6700 Cov.: 33 AF XY: 0.266 AC XY: 19811 AN XY: 74356

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.256

Alfa AF: 0.182 Hom.: 6396

Bravo AF: 0.280

Asia WGS AF: 0.270 AC: 944 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	5.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1853665; hg19: chr6-150298842; COSMIC: COSV57663437;