rs7905174

Variant names:

• chr10-14866242-A-T
• rs7905174
• NM_016299.4:c.994-841A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016299.4(HSPA14):​c.994-841A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,014 control chromosomes in the GnomAD database, including 15,856 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 0.42 (15856 hom., cov: 32)
• Consequence: HSPA14 NM_016299.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 4 publications found

Genes affected

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]

SUV39H2-DT (HGNC:55188): (SUV39H2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA14	NM_016299.4	c.994-841A>T		intron_variant	Intron 10 of 13	ENST00000378372.8	NP_057383.2
SUV39H2-DT	NR_199703.1	n.540T>A		non_coding_transcript_exon_variant	Exon 3 of 3
SUV39H2-DT	NR_199704.1	n.817T>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA14	ENST00000378372.8	c.994-841A>T		intron_variant	Intron 10 of 13	1	NM_016299.4	ENSP00000367623.3
SUV39H2-DT	ENST00000731019.1	n.401+1475T>A		intron_variant	Intron 2 of 2
SUV39H2-DT	ENST00000731020.1	n.435+1475T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63686 AN: 151896 Hom.: 15810 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.420 AC: 63790 AN: 152014 Hom.: 15856 Cov.: 32 AF XY: 0.421 AC XY: 31276 AN XY: 74318

African (AFR) AF: 0.696 AC: 28832 AN: 41418

American (AMR) AF: 0.375 AC: 5734 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2174 AN: 5166

South Asian (SAS) AF: 0.497 AC: 2396 AN: 4818

European-Finnish (FIN) AF: 0.237 AC: 2512 AN: 10584

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19576 AN: 67962

Other (OTH) AF: 0.376 AC: 792 AN: 2108

Alfa AF: 0.362 Hom.: 1459

Bravo AF: 0.439

Asia WGS AF: 0.428 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.41
PhyloP100		-1.3
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: rs7905174; hg19: chr10-14908241;