rs1869641

Positions:

• chr6-98829991-C-T

Variant summary

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

The ENST00000635423.1(ENSG00000283010):​n.969G>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 0.372 in 151,802 control chromosomes in the GnomAD database, including 10,766 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 0.37 (10766 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENST00000635423.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000635423.1	n.969G>A		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56474 AN: 151684 Hom.: 10769 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.360

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.372 AC: 56500 AN: 151802 Hom.: 10766 Cov.: 31 AF XY: 0.373 AC XY: 27658 AN XY: 74194

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.358

Alfa AF: 0.384 Hom.: 10803

Bravo AF: 0.364

Asia WGS AF: 0.207 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869641; hg19: chr6-99277867;