rs7905174

chr10-14866242-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC124902382 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
HSPA14	NM_016299.4	c.994-841A>T		intron_variant		ENST00000378372.8
LOC124902382	XR_007062064.1	n.540T>A		non_coding_transcript_exon_variant	3/3
LOC124902382	XR_007062065.1	n.817T>A		non_coding_transcript_exon_variant	3/3
LOC124902382	XR_007062066.1	n.393-92T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA14	ENST00000378372.8	c.994-841A>T		intron_variant		1	NM_016299.4	P1

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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.376

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

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: rs7905174; hg19: chr10-14908241;