rs12770170

Variant names:

• chr10-14846907-T-A
• rs12770170
• NM_001378785.1:c.*3013T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-14846907-T-A
• chr10-14846907-T-C

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

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

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.*3013T>A		3_prime_UTR	Exon 5 of 5	NP_001365714.1	A0A1W2PQ72
	HSPA14	NM_016299.4	MANE Select	c.222-1702T>A		intron	N/A	NP_057383.2	Q0VDF9
	MSANTD7	NM_001378790.1		c.*3013T>A		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.*3013T>A		3_prime_UTR	Exon 5 of 5	ENSP00000491568.1	A0A1W2PQ72
	HSPA14	ENST00000378372.8	TSL:1 MANE Select	c.222-1702T>A		intron	N/A	ENSP00000367623.3	Q0VDF9
	HSPA14	ENST00000441647.1	TSL:3	c.186-1702T>A		intron	N/A	ENSP00000404691.1	H7C2A1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.2
DANN	Benign	0.75
PhyloP100		1.4

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: rs12770170; hg19: chr10-14888906;