chr11-18634724-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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]

ENSG00000307133 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543776.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPTY2D1	ENST00000543776.1	TSL:4	n.68G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000307133	ENST00000824036.1		n.138C>T		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AF: 0.141 AC: 56 AN: 396

American (AMR) AF: 0.647 AC: 1423 AN: 2200

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 108 AN: 152

East Asian (EAS) AF: 0.407 AC: 255 AN: 626

South Asian (SAS) AF: 0.630 AC: 1987 AN: 3156

European-Finnish (FIN) AF: 0.575 AC: 100 AN: 174

Middle Eastern (MID) AF: 0.727 AC: 16 AN: 22

European-Non Finnish (NFE) AF: 0.719 AC: 4067 AN: 5658

Other (OTH) AF: 0.666 AC: 301 AN: 452

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

African (AFR) AF: 0.203 AC: 8410 AN: 41530

American (AMR) AF: 0.661 AC: 10101 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2594 AN: 3464

East Asian (EAS) AF: 0.502 AC: 2591 AN: 5160

South Asian (SAS) AF: 0.609 AC: 2937 AN: 4824

European-Finnish (FIN) AF: 0.593 AC: 6265 AN: 10566

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49983 AN: 67958

Other (OTH) AF: 0.593 AC: 1249 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.6
DANN	Benign	0.92
PhyloP100		-0.36
PromoterAI		0.0063	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10832962; hg19: chr11-18656271;