rs11246311

Positions:

• chr11-783512-A-C

Variant summary

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

The NR_126342.1(GATD1-DT):​n.225-18A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 191,156 control chromosomes in the GnomAD database, including 771 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 0.072 (576 hom., cov: 32)
  • Exomes 𝑓: 0.082 (195 hom.)
• Consequence: GATD1-DT NR_126342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

Genes affected

GATD1-DT (HGNC:29907): (GATD1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATD1-DT	NR_126342.1	n.225-18A>C		intron_variant, non_coding_transcript_variant
GATD1-DT	NR_126343.1	n.119-18A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATD1-DT	ENST00000530083.3	n.123-18A>C		intron_variant, non_coding_transcript_variant		3
GATD1-DT	ENST00000525941.1	n.195-18A>C		intron_variant, non_coding_transcript_variant		2
GATD1-DT	ENST00000701716.1	n.105-18A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0724 AC: 10999 AN: 152018 Hom.: 577 Cov.: 32

Gnomad AFR AF: 0.0192

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0751

GnomAD4 exome AF: 0.0819 AC: 3197 AN: 39030 Hom.: 195 Cov.: 0 AF XY: 0.0753 AC XY: 1571 AN XY: 20866

Gnomad4 AFR exome AF: 0.0133

Gnomad4 AMR exome AF: 0.0376

Gnomad4 ASJ exome AF: 0.0636

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0297

Gnomad4 FIN exome AF: 0.0836

Gnomad4 NFE exome AF: 0.108

Gnomad4 OTH exome AF: 0.0791

GnomAD4 genome AF: 0.0723 AC: 10998 AN: 152126 Hom.: 576 Cov.: 32 AF XY: 0.0693 AC XY: 5155 AN XY: 74360

Gnomad4 AFR AF: 0.0192

Gnomad4 AMR AF: 0.0608

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0325

Gnomad4 FIN AF: 0.0931

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0735

Alfa AF: 0.0994 Hom.: 1097

Bravo AF: 0.0655

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11246311; hg19: chr11-783512;