rs17101915

chr14-64535232-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_110550.1(HSPA2-AS1):n.53-2663C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 152,158 control chromosomes in the GnomAD database, including 45 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 0.022 (45 hom., cov: 32)
• Consequence: HSPA2-AS1 NR_110550.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

Genes affected

HSPA2-AS1 (HGNC:55433): (HSPA2 and ZBTB1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0224 (3411/152158) while in subpopulation NFE AF= 0.0279 (1896/68012). AF 95% confidence interval is 0.0268. There are 45 homozygotes in gnomad4. There are 1598 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 44 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA2-AS1	NR_110550.1	n.53-2663C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA2-AS1	ENST00000554918.1	n.53-2663C>A		intron_variant, non_coding_transcript_variant		3
HSPA2-AS1	ENST00000648003.1	n.475-2663C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 3406 AN: 152042 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0178

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0279

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0224 AC: 3411 AN: 152158 Hom.: 45 Cov.: 32 AF XY: 0.0215 AC XY: 1598 AN XY: 74370

Gnomad4 AFR AF: 0.0195

Gnomad4 AMR AF: 0.0178

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.0182

Gnomad4 NFE AF: 0.0279

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0276 Hom.: 10

Bravo AF: 0.0216

Asia WGS AF: 0.00953 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	9.3
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17101915; hg19: chr14-65001950;