rs1401

Positions:

• chr6-169033633-C-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: ENST00000623089.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000623089.1	n.253C>T		non_coding_transcript_exon_variant	1/1

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;