11-106020872-C-T

Variant names:

• chr11-106020872-C-T
• rs2249950
• NM_032424.3:c.-151+90G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032424.3(MSANTD4):​c.-151+90G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,054 control chromosomes in the GnomAD database, including 41,572 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 0.74 (41572 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: MSANTD4 NM_032424.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 3 publications found

Genes affected

MSANTD4 (HGNC:29383): (Myb/SANT DNA binding domain containing 4 with coiled-coils) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSANTD4	NM_032424.3	c.-151+90G>A		intron_variant	Intron 1 of 2	ENST00000301919.9	NP_115800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSANTD4	ENST00000301919.9	c.-151+90G>A		intron_variant	Intron 1 of 2	1	NM_032424.3	ENSP00000304713.4
MSANTD4	ENST00000530788.1	c.-151+1323G>A		intron_variant	Intron 1 of 2	1		ENSP00000435125.1
MSANTD4	ENST00000534458.1	c.-151+1250G>A		intron_variant	Intron 1 of 1	4		ENSP00000432245.1
MSANTD4	ENST00000530108.1	c.-151+964G>A		intron_variant	Intron 1 of 1	2		ENSP00000435372.1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112279 AN: 151938 Hom.: 41550 Cov.: 33

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.739 AC: 112339 AN: 152054 Hom.: 41572 Cov.: 33 AF XY: 0.733 AC XY: 54485 AN XY: 74312

African (AFR) AF: 0.741 AC: 30702 AN: 41458

American (AMR) AF: 0.727 AC: 11103 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2406 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3017 AN: 5154

South Asian (SAS) AF: 0.725 AC: 3495 AN: 4824

European-Finnish (FIN) AF: 0.702 AC: 7405 AN: 10550

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51757 AN: 68002

Other (OTH) AF: 0.729 AC: 1539 AN: 2112

Alfa AF: 0.749 Hom.: 174562

Bravo AF: 0.740

Asia WGS AF: 0.663 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.19
PhyloP100		-0.042
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2249950; hg19: chr11-105891599;