rs1055368

Variant names:

• chr6-906962-C-A
• rs1055368
• ENST00000620188.1:n.448G>T

Your query was ambiguous. Multiple possible variants found:

• 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: ENSG00000276687 ENST00000620188.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

ENSG00000276687 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000276687	ENST00000620188.1	n.448G>T		non_coding_transcript_exon_variant	Exon 2 of 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;