20-3747379-C-T

Variant names:

• chr20-3747379-C-T
• rs674110
• NM_052970.5:c.676-838C>T

Variant summary

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

The NM_052970.5(HSPA12B):​c.676-838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,216 control chromosomes in the GnomAD database, including 65,641 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 0.93 (65641 hom., cov: 32)
• Consequence: HSPA12B NM_052970.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 2 publications found

Genes affected

HSPA12B (HGNC:16193): (heat shock protein family A (Hsp70) member 12B) The protein encoded by this gene contains an atypical heat shock protein 70 (Hsp70) ATPase domain and is therefore a distant member of the mammalian Hsp70 family. This gene may be involved in susceptibility to atherosclerosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA12B	NM_052970.5	c.676-838C>T		intron_variant	Intron 7 of 12	ENST00000254963.7	NP_443202.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA12B	ENST00000254963.7	c.676-838C>T		intron_variant	Intron 7 of 12	1	NM_052970.5	ENSP00000254963.2
HSPA12B	ENST00000399701.1	c.418-838C>T		intron_variant	Intron 6 of 11	1		ENSP00000382608.1

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141103 AN: 152098 Hom.: 65586 Cov.: 32

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.937

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.928 AC: 141218 AN: 152216 Hom.: 65641 Cov.: 32 AF XY: 0.926 AC XY: 68869 AN XY: 74398

African (AFR) AF: 0.914 AC: 37949 AN: 41520

American (AMR) AF: 0.964 AC: 14757 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 3281 AN: 3472

East Asian (EAS) AF: 0.752 AC: 3886 AN: 5170

South Asian (SAS) AF: 0.982 AC: 4741 AN: 4830

European-Finnish (FIN) AF: 0.901 AC: 9540 AN: 10592

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63958 AN: 68012

Other (OTH) AF: 0.936 AC: 1976 AN: 2110

Alfa AF: 0.941 Hom.: 125595

Bravo AF: 0.930

Asia WGS AF: 0.889 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs674110; hg19: chr20-3728026;