NM_001378785.1:c.*3013T>A

Variant names:

• chr10-14846907-T-A
• NM_001378785.1:c.*3013T>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001378785.1(MSANTD7):​c.*3013T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: MSANTD7 NM_001378785.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSANTD7	NM_001378785.1	c.*3013T>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000640019.3	NP_001365714.1
HSPA14	NM_016299.4	c.222-1702T>A		intron_variant	Intron 3 of 13	ENST00000378372.8	NP_057383.2
MSANTD7	NM_001378790.1	c.*3013T>A		3_prime_UTR_variant	Exon 4 of 4		NP_001365719.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSANTD7	ENST00000640019.3	c.*3013T>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_001378785.1	ENSP00000491568.1
HSPA14	ENST00000378372.8	c.222-1702T>A		intron_variant	Intron 3 of 13	1	NM_016299.4	ENSP00000367623.3
HSPA14	ENST00000441647.1	c.186-1702T>A		intron_variant	Intron 3 of 5	3		ENSP00000404691.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.2
DANN	Benign	0.75

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-14888906;