chr6-169033633-C-T

Variant names:

• chr6-169033633-C-T
• rs1401
• ENST00000623089.1:n.253C>T

Variant summary

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

The ENST00000623089.1(ENSG00000279810):​n.253C>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 0.243 in 152,142 control chromosomes in the GnomAD database, including 5,429 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 0.24 (5428 hom., cov: 31)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: ENSG00000279810 ENST00000623089.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

ENSG00000279810 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 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
ENSG00000279810	ENST00000623089.1	n.253C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37018 AN: 152000 Hom.: 5426 Cov.: 31

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.308 AC: 8 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.227 AC XY: 5 AN XY: 22

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.243 AC: 37036 AN: 152116 Hom.: 5428 Cov.: 31 AF XY: 0.243 AC XY: 18097 AN XY: 74328

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.274

Alfa AF: 0.272 Hom.: 1000

Bravo AF: 0.241

Asia WGS AF: 0.241 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1401; hg19: chr6-169433728; COSMIC: COSV69502670;