rs11218942

Variant names:

• chr11-123063042-C-A
• rs11218942
• ENST00000525624.5:c.-298G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-123063042-C-A
• chr11-123063042-C-G
• chr11-123063042-C-T

Variant summary

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

The ENST00000525624.5(HSPA8):​c.-298G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 152,200 control chromosomes in the GnomAD database, including 371 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 (371 hom., cov: 33)
  • Exomes 𝑓: 0.031 (0 hom.)
• Consequence: HSPA8 ENST00000525624.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525624.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA8	ENST00000525624.5	TSL:5	c.-298G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 4	ENSP00000435154.1
	ENSG00000288061	ENST00000690490.3		n.550C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288061	ENST00000836650.1		n.404C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9707 AN: 152050 Hom.: 371 Cov.: 33

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0520

Gnomad FIN AF: 0.0620

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0632

GnomAD4 exome AF: 0.0313 AC: 1 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.0333 AC XY: 1 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0333 AC: 1 AN: 30

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0639 AC: 9719 AN: 152168 Hom.: 371 Cov.: 33 AF XY: 0.0682 AC XY: 5071 AN XY: 74400

African (AFR) AF: 0.0563 AC: 2338 AN: 41524

American (AMR) AF: 0.130 AC: 1991 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0776 AC: 269 AN: 3468

East Asian (EAS) AF: 0.126 AC: 648 AN: 5142

South Asian (SAS) AF: 0.0527 AC: 254 AN: 4824

European-Finnish (FIN) AF: 0.0620 AC: 657 AN: 10596

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0500 AC: 3403 AN: 68008

Other (OTH) AF: 0.0644 AC: 136 AN: 2112

Alfa AF: 0.0194 Hom.: 11

Bravo AF: 0.0727

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.66
DANN	Benign	0.53
PhyloP100		-1.3
PromoterAI		0.0017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11218942; hg19: chr11-122933750;