6-88175102-C-T

Position:

• chr6-88175102-C-T

Variant summary

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

The ENST00000624253.1(ENSG00000279565):​n.2842C>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 0.798 in 152,196 control chromosomes in the GnomAD database, including 48,618 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 0.80 (48562 hom., cov: 30)
  • Exomes 𝑓: 0.75 (56 hom.)
• Consequence: ENSG00000279565 ENST00000624253.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

Genes affected

ENSG00000279565 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.88175102C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279565	ENST00000624253.1	n.2842C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121164 AN: 151880 Hom.: 48520 Cov.: 30

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.795

GnomAD4 exome AF: 0.747 AC: 148 AN: 198 Hom.: 56 Cov.: 0 AF XY: 0.771 AC XY: 108 AN XY: 140

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.667

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.763

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.798 AC: 121261 AN: 151998 Hom.: 48562 Cov.: 30 AF XY: 0.795 AC XY: 59078 AN XY: 74296

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.792

Alfa AF: 0.782 Hom.: 60993

Bravo AF: 0.798

Asia WGS AF: 0.730 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406977; hg19: chr6-88884821;