10-14845980-C-T

Variant summary

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

The NM_001378785.1(MSANTD7):c.*2086C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 922,844 control chromosomes in the GnomAD database, including 9,028 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 0.11 (1118 hom., cov: 32)
  • Exomes 𝑓: 0.14 (7910 hom.)
• Consequence: MSANTD7 NM_001378785.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

Genes affected

MSANTD7 (HGNC:56248): (Myb/SANT DNA binding domain containing 7)

HSPA14 (HGNC:29526): (heat shock protein family A (Hsp70) member 14) Predicted to enable several functions, including ATP binding activity; misfolded protein binding activity; and unfolded protein binding activity. Predicted to be involved in several processes, including cellular response to unfolded protein; chaperone cofactor-dependent protein refolding; and protein refolding. Located in cytosol. Colocalizes with ribosome. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSANTD7	NM_001378785.1	c.*2086C>T		3_prime_UTR_variant	5/5	ENST00000640019.3
HSPA14	NM_016299.4	c.222-2629C>T		intron_variant		ENST00000378372.8
MSANTD7	NM_001378790.1	c.*2086C>T		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSANTD7	ENST00000640019.3	c.*2086C>T		3_prime_UTR_variant	5/5	1	NM_001378785.1	P1
HSPA14	ENST00000378372.8	c.222-2629C>T		intron_variant		1	NM_016299.4	P1
HSPA14	ENST00000441647.1	c.188-2629C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16242 AN: 151656 Hom.: 1118 Cov.: 32

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.141 AC: 108439 AN: 771070 Hom.: 7910 Cov.: 12 AF XY: 0.141 AC XY: 50512 AN XY: 357544

Gnomad4 AFR exome AF: 0.0197

Gnomad4 AMR exome AF: 0.115

Gnomad4 ASJ exome AF: 0.0836

Gnomad4 EAS exome AF: 0.00494

Gnomad4 SAS exome AF: 0.0984

Gnomad4 FIN exome AF: 0.111

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.127

GnomAD4 genome AF: 0.107 AC: 16243 AN: 151774 Hom.: 1118 Cov.: 32 AF XY: 0.107 AC XY: 7956 AN XY: 74122

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.106

Alfa AF: 0.127 Hom.: 892

Bravo AF: 0.0997

Asia WGS AF: 0.0520 AC: 180 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.1
Dann	Benign	0.61

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: rs11593057; hg19: chr10-14887979;