6-33208047-A-G

Position:

• chr6-33208047-A-G

Variant summary

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

The ENST00000692840.1(ENSG00000288751):​n.427T>C 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 0.0945 in 334,434 control chromosomes in the GnomAD database, including 2,845 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 0.093 (1201 hom., cov: 32)
  • Exomes 𝑓: 0.095 (1644 hom.)
• Consequence: ENST00000692840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 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
	ENST00000692840.1	n.427T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14180 AN: 152068 Hom.: 1190 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.0852

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0955 AC: 17401 AN: 182248 Hom.: 1644 AF XY: 0.0931 AC XY: 9658 AN XY: 103714

Gnomad4 AFR exome AF: 0.0833

Gnomad4 AMR exome AF: 0.0894

Gnomad4 ASJ exome AF: 0.0447

Gnomad4 EAS exome AF: 0.523

Gnomad4 SAS exome AF: 0.0822

Gnomad4 FIN exome AF: 0.0798

Gnomad4 NFE exome AF: 0.0709

Gnomad4 OTH exome AF: 0.0908

GnomAD4 genome AF: 0.0933 AC: 14198 AN: 152186 Hom.: 1201 Cov.: 32 AF XY: 0.0949 AC XY: 7064 AN XY: 74402

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.0888

Gnomad4 FIN AF: 0.0852

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0828 Hom.: 1598

Bravo AF: 0.0975

Asia WGS AF: 0.241 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.93
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs213210; hg19: chr6-33175824;