rs11024739

chr11-18624296-C-Achr11-18624296-C-G

Variant summary

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

The NM_194285.3(SPTY2D1):c.61-7307G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,968 control chromosomes in the GnomAD database, including 27,733 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 (27733 hom., cov: 32)
• Consequence: SPTY2D1 NM_194285.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494

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=-0.58).
• 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/exons	MANE	UniProt
SPTY2D1	NM_194285.3	c.61-7307G>T		intron_variant		ENST00000336349.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPTY2D1	ENST00000336349.6	c.61-7307G>T		intron_variant		1	NM_194285.3	P1
SPTY2D1	ENST00000536336.5	n.193-7307G>T		intron_variant, non_coding_transcript_variant		2
SPTY2D1	ENST00000543776.1	n.103-7307G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85005 AN: 151856 Hom.: 27733 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.596

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.559 AC: 85000 AN: 151968 Hom.: 27733 Cov.: 32 AF XY: 0.555 AC XY: 41227 AN XY: 74244

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.592

Alfa AF: 0.703 Hom.: 68924

Bravo AF: 0.550

Asia WGS AF: 0.502 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	8.0
Dann	Benign	0.55

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: rs11024739; hg19: chr11-18645843;