chr11-123062094-G-A

Variant names:

• chr11-123062094-G-A
• rs2276075
• ENST00000527983.5:n.114C>T

Variant summary

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

The ENST00000527983.5(HSPA8):​n.114C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0642 in 152,844 control chromosomes in the GnomAD database, including 379 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 0.064 (376 hom., cov: 33)
  • Exomes 𝑓: 0.055 (3 hom.)
• Consequence: HSPA8 ENST00000527983.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 10 publications found

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]

ENSG00000288061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527983.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA8	NM_006597.6	MANE Select	c.-36C>T		5_prime_UTR	Exon 1 of 9	NP_006588.1
	HSPA8	NM_153201.4		c.-36C>T		5_prime_UTR	Exon 1 of 8	NP_694881.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA8	ENST00000527983.5	TSL:1	n.114C>T		non_coding_transcript_exon	Exon 1 of 5
	HSPA8	ENST00000534624.6	TSL:1 MANE Select	c.-36C>T		5_prime_UTR	Exon 1 of 9	ENSP00000432083.1
	HSPA8	ENST00000453788.6	TSL:1	c.-36C>T		5_prime_UTR	Exon 1 of 8	ENSP00000404372.2

Frequencies

GnomAD3 genomes AF: 0.0642 AC: 9763 AN: 152004 Hom.: 376 Cov.: 33

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0522

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0638

GnomAD4 exome AF: 0.0554 AC: 40 AN: 722 Hom.: 3 Cov.: 0 AF XY: 0.0566 AC XY: 31 AN XY: 548

African (AFR) AF: 0.0556 AC: 1 AN: 18

American (AMR) AF: 0.167 AC: 2 AN: 12

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 3 AN: 12

South Asian (SAS) AF: 0.0417 AC: 2 AN: 48

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.167 AC: 1 AN: 6

European-Non Finnish (NFE) AF: 0.0500 AC: 30 AN: 600

Other (OTH) AF: 0.0455 AC: 1 AN: 22

GnomAD4 genome AF: 0.0643 AC: 9775 AN: 152122 Hom.: 376 Cov.: 33 AF XY: 0.0685 AC XY: 5094 AN XY: 74344

African (AFR) AF: 0.0549 AC: 2279 AN: 41494

American (AMR) AF: 0.131 AC: 1996 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.130 AC: 670 AN: 5164

South Asian (SAS) AF: 0.0529 AC: 255 AN: 4822

European-Finnish (FIN) AF: 0.0619 AC: 655 AN: 10574

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0513 AC: 3490 AN: 68012

Other (OTH) AF: 0.0651 AC: 137 AN: 2106

Alfa AF: 0.0609 Hom.: 410

Bravo AF: 0.0707

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.48
DANN	Benign	0.72
PhyloP100		-2.6
PromoterAI		-0.098	Neutral
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2276075; hg19: chr11-122932802;