11-123061415-C-G

Position:

• chr11-123061415-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006597.6(HSPA8):​c.-5-86G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 1,037,656 control chromosomes in the GnomAD database, including 30,804 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 0.28 (7122 hom., cov: 32)
  • Exomes 𝑓: 0.22 (23682 hom.)
• Consequence: HSPA8 NM_006597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

HSPA8 (HGNC:5241): (heat shock protein family A (Hsp70) member 8) This gene encodes a member of the heat shock protein 70 family, which contains both heat-inducible and constitutively expressed members. This protein belongs to the latter group, which are also referred to as heat-shock cognate proteins. It functions as a chaperone, and binds to nascent polypeptides to facilitate correct folding. It also functions as an ATPase in the disassembly of clathrin-coated vesicles during transport of membrane components through the cell. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA8	NM_006597.6	c.-5-86G>C		intron_variant		ENST00000534624.6
HSPA8	NM_153201.4	c.-5-86G>C		intron_variant
HSPA8	XM_011542798.2	c.-5-86G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA8	ENST00000534624.6	c.-5-86G>C		intron_variant		1	NM_006597.6	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42310 AN: 151954 Hom.: 7101 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.241

GnomAD4 exome AF: 0.222 AC: 196753 AN: 885584 Hom.: 23682 Cov.: 11 AF XY: 0.224 AC XY: 101724 AN XY: 454936

Gnomad4 AFR exome AF: 0.476

Gnomad4 AMR exome AF: 0.236

Gnomad4 ASJ exome AF: 0.161

Gnomad4 EAS exome AF: 0.440

Gnomad4 SAS exome AF: 0.306

Gnomad4 FIN exome AF: 0.179

Gnomad4 NFE exome AF: 0.196

Gnomad4 OTH exome AF: 0.238

GnomAD4 genome AF: 0.279 AC: 42389 AN: 152072 Hom.: 7122 Cov.: 32 AF XY: 0.279 AC XY: 20767 AN XY: 74340

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.240

Alfa AF: 0.0987 Hom.: 142

Bravo AF: 0.291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10892958; hg19: chr11-122932123;