chr6-79854802-T-C

Position:

• chr6-79854802-T-C

Variant summary

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

The ENST00000403623.1(ENSG00000220918):​n.119T>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 0.361 in 151,894 control chromosomes in the GnomAD database, including 10,639 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 0.36 (10638 hom., cov: 32)
  • Exomes 𝑓: 0.30 (1 hom.)
• Consequence: ENSG00000220918 ENST00000403623.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

ENSG00000220918 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100422671		n.79854802T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000220918	ENST00000403623.1	n.119T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54841 AN: 151756 Hom.: 10627 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.300 AC: 6 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 4 AN XY: 16

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.361 AC: 54892 AN: 151874 Hom.: 10638 Cov.: 32 AF XY: 0.362 AC XY: 26853 AN XY: 74196

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.386

Alfa AF: 0.387 Hom.: 20101

Bravo AF: 0.368

Asia WGS AF: 0.484 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
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: rs9341799; hg19: chr6-80564519;