11-68030238-C-G

Variant names:

• chr11-68030238-C-G
• rs10896288
• ENST00000532296.1:n.203+21G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532296.1(GLTC1):​n.203+21G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,838 control chromosomes in the GnomAD database, including 18,521 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 0.45 (18458 hom., cov: 30)
  • Exomes 𝑓: 0.64 (63 hom.)
• Consequence: GLTC1 ENST00000532296.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 5 publications found

Genes affected

GLTC1 (HGNC:56861):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532296.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLTC1	NR_197583.1		n.142+55G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLTC1	ENST00000532296.1	TSL:3	n.203+21G>C		intron	N/A
	GLTC1	ENST00000828081.1		n.104+55G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68421 AN: 151448 Hom.: 18457 Cov.: 30

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.499

GnomAD4 exome AF: 0.639 AC: 175 AN: 274 Hom.: 63 Cov.: 0 AF XY: 0.656 AC XY: 143 AN XY: 218

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.677 AC: 130 AN: 192

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.586 AC: 41 AN: 70

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.451 AC: 68416 AN: 151564 Hom.: 18458 Cov.: 30 AF XY: 0.459 AC XY: 33994 AN XY: 74024

African (AFR) AF: 0.132 AC: 5434 AN: 41288

American (AMR) AF: 0.583 AC: 8886 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2061 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2854 AN: 5152

South Asian (SAS) AF: 0.681 AC: 3274 AN: 4808

European-Finnish (FIN) AF: 0.573 AC: 5968 AN: 10424

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38210 AN: 67884

Other (OTH) AF: 0.503 AC: 1057 AN: 2100

Alfa AF: 0.378 Hom.: 1201

Bravo AF: 0.437

Asia WGS AF: 0.584 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.8
DANN	Benign	0.74
PhyloP100		0.031
PromoterAI		0.0078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10896288; hg19: chr11-67797705;