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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902775	XR_007062927.1	n.381C>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA8	ENST00000525624.5	c.-298G>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 4	5		ENSP00000435154.1
ENSG00000288061	ENST00000690490.3	n.550C>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000288061	ENST00000836650.1	n.404C>A		non_coding_transcript_exon_variant	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 v4.3

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;