11-68683779-C-T

Position:

• chr11-68683779-C-T

Variant summary

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

The ENST00000538401.1(GAL):​n.1C>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 0.658 in 152,378 control chromosomes in the GnomAD database, including 34,858 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 0.66 (34810 hom., cov: 34)
  • Exomes 𝑓: 0.77 (48 hom.)
• Consequence: GAL ENST00000538401.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.62

Genes affected

GAL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984343	XR_001748281.1	n.230+4062G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAL	ENST00000538401.1	n.1C>T		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100145 AN: 152098 Hom.: 34797 Cov.: 34

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.660

GnomAD4 exome AF: 0.772 AC: 125 AN: 162 Hom.: 48 Cov.: 0 AF XY: 0.786 AC XY: 88 AN XY: 112

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.900

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.762

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.658 AC: 100183 AN: 152216 Hom.: 34810 Cov.: 34 AF XY: 0.670 AC XY: 49833 AN XY: 74424

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.664

Alfa AF: 0.670 Hom.: 4671

Bravo AF: 0.632

Asia WGS AF: 0.801 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4432027; hg19: chr11-68451247;