rs2858087

Variant names:

• chr4-3267165-T-A
• rs2858087
• ENST00000505599.5:n.*103-595T>A

Variant summary

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

The ENST00000505599.5(MSANTD1):​n.*103-595T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,116 control chromosomes in the GnomAD database, including 18,987 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 0.47 (18987 hom., cov: 32)
• Consequence: MSANTD1 ENST00000505599.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

MSANTD1 (HGNC:33741): (Myb/SANT DNA binding domain containing 1) Predicted to be involved in positive regulation of transcription, DNA-templated. Predicted to be active in nuclear body. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSANTD1	ENST00000505599.5	n.*103-595T>A		intron_variant	Intron 4 of 5	2		ENSP00000425405.1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71772 AN: 151998 Hom.: 18978 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.472 AC: 71802 AN: 152116 Hom.: 18987 Cov.: 32 AF XY: 0.474 AC XY: 35217 AN XY: 74370

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.477

Alfa AF: 0.521 Hom.: 2739

Bravo AF: 0.447

Asia WGS AF: 0.417 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858087; hg19: chr4-3268892;