6-98829991-C-T

Variant names:

• chr6-98829991-C-T
• rs1869641
• ENST00000635423.1:n.969G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000283010 ENST00000635423.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540
• Publications: 7 publications found

Genes affected

ENSG00000283010 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PNKY	NR_148381.1	n.*150G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283010	ENST00000635423.1	n.969G>A		non_coding_transcript_exon_variant	Exon 3 of 3	5
ENSG00000309555	ENST00000841996.1	n.93+5743G>A		intron_variant	Intron 1 of 2
ENSG00000283010	ENST00000842171.1	n.*133G>A		downstream_gene_variant

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.373 AC: 15414 AN: 41344

American (AMR) AF: 0.343 AC: 5238 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1091 AN: 3472

East Asian (EAS) AF: 0.166 AC: 854 AN: 5158

South Asian (SAS) AF: 0.293 AC: 1411 AN: 4820

European-Finnish (FIN) AF: 0.442 AC: 4635 AN: 10486

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26663 AN: 67950

Other (OTH) AF: 0.358 AC: 754 AN: 2106

Alfa AF: 0.382 Hom.: 27820

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
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1869641; hg19: chr6-99277867;