rs1853639

Variant names:

• chr6-86897124-G-A
• rs1853639
• ENST00000468100.1:n.7G>A

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000217769	ENST00000468100.1	n.7G>A		non_coding_transcript_exon_variant	Exon 1 of 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;