10-14845980-C-T

Variant names:

• chr10-14845980-C-T
• rs11593057
• NM_001378785.1:c.*2086C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378785.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSANTD7	NM_001378785.1	MANE Select	c.*2086C>T		3_prime_UTR	Exon 5 of 5	NP_001365714.1	A0A1W2PQ72
	HSPA14	NM_016299.4	MANE Select	c.222-2629C>T		intron	N/A	NP_057383.2	Q0VDF9
	MSANTD7	NM_001378790.1		c.*2086C>T		3_prime_UTR	Exon 4 of 4	NP_001365719.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSANTD7	ENST00000640019.3	TSL:1 MANE Select	c.*2086C>T		3_prime_UTR	Exon 5 of 5	ENSP00000491568.1	A0A1W2PQ72
	HSPA14	ENST00000378372.8	TSL:1 MANE Select	c.222-2629C>T		intron	N/A	ENSP00000367623.3	Q0VDF9
	HSPA14	ENST00000441647.1	TSL:3	c.186-2629C>T		intron	N/A	ENSP00000404691.1	H7C2A1

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

African (AFR) AF: 0.0197 AC: 292 AN: 14800

American (AMR) AF: 0.115 AC: 105 AN: 912

Ashkenazi Jewish (ASJ) AF: 0.0836 AC: 401 AN: 4794

East Asian (EAS) AF: 0.00494 AC: 17 AN: 3442

South Asian (SAS) AF: 0.0984 AC: 1504 AN: 15286

European-Finnish (FIN) AF: 0.111 AC: 28 AN: 252

Middle Eastern (MID) AF: 0.144 AC: 214 AN: 1490

European-Non Finnish (NFE) AF: 0.146 AC: 102673 AN: 704806

Other (OTH) AF: 0.127 AC: 3205 AN: 25288

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

African (AFR) AF: 0.0306 AC: 1267 AN: 41360

American (AMR) AF: 0.112 AC: 1703 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3466

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5170

South Asian (SAS) AF: 0.101 AC: 485 AN: 4806

European-Finnish (FIN) AF: 0.152 AC: 1595 AN: 10474

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10450 AN: 67918

Other (OTH) AF: 0.106 AC: 224 AN: 2112

Alfa AF: 0.127 Hom.: 1117

Bravo AF: 0.0997

Asia WGS AF: 0.0520 AC: 180 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		0.023
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11593057;

hg19: chr10-14887979;