ENST00000543776.1:n.68G>A

Variant names:

• chr11-18634724-C-T
• rs10832962
• ENST00000543776.1:n.68G>A

Variant summary

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

The ENST00000543776.1(SPTY2D1):​n.68G>A 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 0.566 in 164,930 control chromosomes in the GnomAD database, including 30,659 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 0.56 (27754 hom., cov: 32)
  • Exomes 𝑓: 0.65 (2905 hom.)
• Consequence: SPTY2D1 ENST00000543776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

SPTY2D1 (HGNC:26818): (SPT2 chromatin protein domain containing 1) Enables DNA binding activity and histone binding activity. Involved in nucleosome organization; regulation of chromatin assembly; and regulation of transcription, DNA-templated. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC105376578 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376578	XR_931097.3	n.376C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPTY2D1	ENST00000543776.1	n.68G>A		non_coding_transcript_exon_variant	Exon 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85056 AN: 151976 Hom.: 27754 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.597

GnomAD4 exome AF: 0.648 AC: 8313 AN: 12836 Hom.: 2905 Cov.: 0 AF XY: 0.643 AC XY: 4735 AN XY: 7368

Gnomad4 AFR exome AF: 0.141

Gnomad4 AMR exome AF: 0.647

Gnomad4 ASJ exome AF: 0.711

Gnomad4 EAS exome AF: 0.407

Gnomad4 SAS exome AF: 0.630

Gnomad4 FIN exome AF: 0.575

Gnomad4 NFE exome AF: 0.719

Gnomad4 OTH exome AF: 0.666

GnomAD4 genome AF: 0.559 AC: 85051 AN: 152094 Hom.: 27754 Cov.: 32 AF XY: 0.555 AC XY: 41275 AN XY: 74350

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.593

Alfa AF: 0.610 Hom.: 4459

Bravo AF: 0.550

Asia WGS AF: 0.501 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.6
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10832962; hg19: chr11-18656271;