rs1853639

Positions:

• chr6-86897124-G-A
• chr6-86897124-G-C

Variant summary

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

The ENST00000468100.1(ENSG00000217769):​n.7G>A 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 0.629 in 1,594,678 control chromosomes in the GnomAD database, including 316,515 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 0.64 (31098 hom., cov: 32)
  • Exomes 𝑓: 0.63 (285417 hom.)
• Consequence: ENSG00000217769 ENST00000468100.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

Genes affected

ENSG00000217769 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86897124G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000217769	ENST00000468100.1	n.7G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96991 AN: 151904 Hom.: 31051 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.613

GnomAD4 exome AF: 0.628 AC: 906466 AN: 1442656 Hom.: 285417 Cov.: 33 AF XY: 0.627 AC XY: 450253 AN XY: 718194

Gnomad4 AFR exome AF: 0.627

Gnomad4 AMR exome AF: 0.720

Gnomad4 ASJ exome AF: 0.641

Gnomad4 EAS exome AF: 0.553

Gnomad4 SAS exome AF: 0.588

Gnomad4 FIN exome AF: 0.659

Gnomad4 NFE exome AF: 0.629

Gnomad4 OTH exome AF: 0.625

GnomAD4 genome AF: 0.639 AC: 97095 AN: 152022 Hom.: 31098 Cov.: 32 AF XY: 0.641 AC XY: 47582 AN XY: 74286

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.608

Alfa AF: 0.641 Hom.: 3855

Bravo AF: 0.638

Asia WGS AF: 0.591 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1853639; hg19: chr6-87606842;