rs7151976

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000394709.2(HSPA2):​c.-6+1198A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 151,930 control chromosomes in the GnomAD database, including 31,944 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 0.63 ( 31944 hom., cov: 31)

Consequence

HSPA2
ENST00000394709.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.475
Variant links:
Genes affected
HSPA2 (HGNC:5235): (heat shock protein family A (Hsp70) member 2) Enables disordered domain specific binding activity; enzyme binding activity; and unfolded protein binding activity. Involved in negative regulation of inclusion body assembly and protein refolding. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
HSPA2-AS1 (HGNC:55433): (HSPA2 and ZBTB1 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HSPA2-AS1NR_110550.1 linkuse as main transcriptn.52+3144T>G intron_variant, non_coding_transcript_variant
HSPA2NM_001387931.1 linkuse as main transcriptc.-6+1198A>C intron_variant NP_001374860.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HSPA2ENST00000394709.2 linkuse as main transcriptc.-6+1198A>C intron_variant 1 ENSP00000378199 P1
HSPA2-AS1ENST00000554918.1 linkuse as main transcriptn.52+3144T>G intron_variant, non_coding_transcript_variant 3
HSPA2-AS1ENST00000648003.1 linkuse as main transcriptn.474+1975T>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.635
AC:
96368
AN:
151812
Hom.:
31930
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.435
Gnomad AMI
AF:
0.737
Gnomad AMR
AF:
0.706
Gnomad ASJ
AF:
0.656
Gnomad EAS
AF:
0.857
Gnomad SAS
AF:
0.715
Gnomad FIN
AF:
0.835
Gnomad MID
AF:
0.596
Gnomad NFE
AF:
0.684
Gnomad OTH
AF:
0.635
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.635
AC:
96406
AN:
151930
Hom.:
31944
Cov.:
31
AF XY:
0.646
AC XY:
47929
AN XY:
74238
show subpopulations
Gnomad4 AFR
AF:
0.435
Gnomad4 AMR
AF:
0.706
Gnomad4 ASJ
AF:
0.656
Gnomad4 EAS
AF:
0.856
Gnomad4 SAS
AF:
0.714
Gnomad4 FIN
AF:
0.835
Gnomad4 NFE
AF:
0.684
Gnomad4 OTH
AF:
0.636
Alfa
AF:
0.626
Hom.:
4393
Bravo
AF:
0.615
Asia WGS
AF:
0.719
AC:
2502
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
8.2
DANN
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7151976; hg19: chr14-65003891; API