rs2858087

Positions:

• chr4-3267165-T-A

Variant summary

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

The ENST00000505599.5(MSANTD1):​c.*103-595T>A variant causes a intron, NMD transcript 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, NMD_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSANTD1	ENST00000505599.5	c.*103-595T>A		intron_variant, NMD_transcript_variant		2		ENSP00000425405

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;