11-106016262-C-T

Variant names:

• chr11-106016262-C-T
• rs1939810
• NM_032424.3:c.-151+4700G>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+4700G>A 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 152,016 control chromosomes in the GnomAD database, including 24,220 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 (24220 hom., cov: 32)
• Consequence: MSANTD4 NM_032424.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSANTD4	NM_032424.3	c.-151+4700G>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+4700G>A		intron_variant	Intron 1 of 2	1	NM_032424.3	ENSP00000304713.4
MSANTD4	ENST00000530788.1	c.-150-5195G>A		intron_variant	Intron 1 of 2	1		ENSP00000435125.1
MSANTD4	ENST00000534458.1	c.-150-5195G>A		intron_variant	Intron 1 of 1	4		ENSP00000432245.1
MSANTD4	ENST00000530108.1	c.-150-5195G>A		intron_variant	Intron 1 of 1	2		ENSP00000435372.1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84935 AN: 151898 Hom.: 24219 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.559 AC: 84956 AN: 152016 Hom.: 24220 Cov.: 32 AF XY: 0.555 AC XY: 41271 AN XY: 74308

African (AFR) AF: 0.446 AC: 18479 AN: 41442

American (AMR) AF: 0.602 AC: 9198 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2937 AN: 5176

South Asian (SAS) AF: 0.614 AC: 2962 AN: 4824

European-Finnish (FIN) AF: 0.534 AC: 5636 AN: 10552

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42006 AN: 67950

Other (OTH) AF: 0.561 AC: 1187 AN: 2114

Alfa AF: 0.596 Hom.: 80418

Bravo AF: 0.561

Asia WGS AF: 0.564 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.51
PhyloP100		0.071
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: rs1939810; hg19: chr11-105886989;