11-18611437-T-C

Position:

• chr11-18611437-T-C

Variant summary

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

The ENST00000336349.6(SPTY2D1):​c.1964+40A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 1,576,072 control chromosomes in the GnomAD database, including 385,991 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 (27689 hom., cov: 33)
  • Exomes 𝑓: 0.70 (358302 hom.)
• Consequence: SPTY2D1 ENST00000336349.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPTY2D1	NM_194285.3	c.1964+40A>G		intron_variant		ENST00000336349.6	NP_919261.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPTY2D1	ENST00000336349.6	c.1964+40A>G		intron_variant		1	NM_194285.3	ENSP00000337991	P1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84992 AN: 151998 Hom.: 27689 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.595

GnomAD3 exomes AF: 0.643 AC: 160544 AN: 249720 Hom.: 54106 AF XY: 0.655 AC XY: 88377 AN XY: 135020

Gnomad AFR exome AF: 0.193

Gnomad AMR exome AF: 0.634

Gnomad ASJ exome AF: 0.742

Gnomad EAS exome AF: 0.503

Gnomad SAS exome AF: 0.631

Gnomad FIN exome AF: 0.601

Gnomad NFE exome AF: 0.733

Gnomad OTH exome AF: 0.678

GnomAD4 exome AF: 0.702 AC: 999354 AN: 1423956 Hom.: 358302 Cov.: 23 AF XY: 0.702 AC XY: 499291 AN XY: 710992

Gnomad4 AFR exome AF: 0.183

Gnomad4 AMR exome AF: 0.639

Gnomad4 ASJ exome AF: 0.745

Gnomad4 EAS exome AF: 0.482

Gnomad4 SAS exome AF: 0.631

Gnomad4 FIN exome AF: 0.609

Gnomad4 NFE exome AF: 0.739

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.559 AC: 84987 AN: 152116 Hom.: 27689 Cov.: 33 AF XY: 0.555 AC XY: 41253 AN XY: 74354

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.591

Alfa AF: 0.704 Hom.: 49689

Bravo AF: 0.549

Asia WGS AF: 0.501 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.5
DANN	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10128711; hg19: chr11-18632984; COSMIC: COSV60473348; COSMIC: COSV60473348;