rs10512270

Positions:

• chr9-100435295-A-G
• chr9-100435295-A-T

Variant summary

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

The NM_080655.3(MSANTD3):​c.-33-6611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,178 control chromosomes in the GnomAD database, including 329 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 0.044 (329 hom., cov: 32)
• Consequence: MSANTD3 NM_080655.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.873

Genes affected

MSANTD3 (HGNC:23370): (Myb/SANT DNA binding domain containing 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSANTD3	NM_080655.3	c.-33-6611A>G		intron_variant		ENST00000395067.7	NP_542386.1
MSANTD3	NM_001198805.2	c.-33-6611A>G		intron_variant			NP_001185734.1
MSANTD3	NM_001198806.2	c.-34+5633A>G		intron_variant			NP_001185735.1
MSANTD3	NM_001198807.2	c.-33-6611A>G		intron_variant			NP_001185736.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSANTD3	ENST00000395067.7	c.-33-6611A>G		intron_variant		1	NM_080655.3	ENSP00000378506.2

Frequencies

GnomAD3 genomes AF: 0.0439 AC: 6670 AN: 152058 Hom.: 332 Cov.: 32

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.00943

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0438 AC: 6660 AN: 152178 Hom.: 329 Cov.: 32 AF XY: 0.0473 AC XY: 3520 AN XY: 74422

Gnomad4 AFR AF: 0.0571

Gnomad4 AMR AF: 0.0328

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.00943

Gnomad4 NFE AF: 0.0205

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0311 Hom.: 112

Bravo AF: 0.0437

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.5
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: rs10512270; hg19: chr9-103197577;