rs1055368

Positions:

• chr6-906962-C-A
• chr6-906962-C-T

Variant summary

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

The ENST00000620188.1(ENSG00000276687):​n.448G>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 0.568 in 152,024 control chromosomes in the GnomAD database, including 25,144 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 0.57 (25143 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENST00000620188.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

(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 = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000620188.1	n.448G>T		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86206 AN: 151904 Hom.: 25114 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.564

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 ASJ exome AF: 1.00

GnomAD4 genome AF: 0.568 AC: 86283 AN: 152022 Hom.: 25143 Cov.: 32 AF XY: 0.568 AC XY: 42181 AN XY: 74300

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.564

Alfa AF: 0.506 Hom.: 16726

Bravo AF: 0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1055368; hg19: chr6-907550;