rs11246311

Variant names:

• chr11-783512-A-C
• rs11246311
• ENST00000525941.2:n.231-18A>C

Variant summary

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

The ENST00000525941.2(GATD1-DT):​n.231-18A>C variant causes a intron 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 ENST00000525941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525941.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATD1-DT	NR_126342.1		n.225-18A>C		intron	N/A
	GATD1-DT	NR_126343.1		n.119-18A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATD1-DT	ENST00000525941.2	TSL:2	n.231-18A>C		intron	N/A
	GATD1-DT	ENST00000530083.3	TSL:3	n.123-18A>C		intron	N/A
	GATD1-DT	ENST00000701716.2		n.127-18A>C		intron	N/A

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

African (AFR) AF: 0.0133 AC: 6 AN: 450

American (AMR) AF: 0.0376 AC: 61 AN: 1624

Ashkenazi Jewish (ASJ) AF: 0.0636 AC: 51 AN: 802

East Asian (EAS) AF: 0.00 AC: 0 AN: 766

South Asian (SAS) AF: 0.0297 AC: 234 AN: 7882

European-Finnish (FIN) AF: 0.0836 AC: 186 AN: 2224

Middle Eastern (MID) AF: 0.0423 AC: 6 AN: 142

European-Non Finnish (NFE) AF: 0.108 AC: 2485 AN: 23016

Other (OTH) AF: 0.0791 AC: 168 AN: 2124

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

African (AFR) AF: 0.0192 AC: 795 AN: 41512

American (AMR) AF: 0.0608 AC: 929 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0325 AC: 157 AN: 4824

European-Finnish (FIN) AF: 0.0931 AC: 983 AN: 10560

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7688 AN: 67992

Other (OTH) AF: 0.0735 AC: 155 AN: 2110

Alfa AF: 0.0909 Hom.: 1773

Bravo AF: 0.0655

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.49
PhyloP100		0.38
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11246311; hg19: chr11-783512;