rs17101915

Variant names:

• chr14-64535232-G-T
• rs17101915
• ENST00000554918.1:n.53-2663C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000554918.1(HSPA2-AS1):​n.53-2663C>A variant causes a intron 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 ENST00000554918.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 45 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA2-AS1	NR_110550.1	n.53-2663C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA2-AS1	ENST00000554918.1	n.53-2663C>A		intron_variant	Intron 1 of 3	3
HSPA2-AS1	ENST00000648003.1	n.475-2663C>A		intron_variant	Intron 1 of 3
HSPA2-AS1	ENST00000846147.1	n.54-2663C>A		intron_variant	Intron 1 of 3
HSPA2-AS1	ENST00000846148.1	n.51-2670C>A		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.0195 AC: 808 AN: 41500

American (AMR) AF: 0.0178 AC: 272 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 47 AN: 3464

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4812

European-Finnish (FIN) AF: 0.0182 AC: 193 AN: 10578

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0279 AC: 1896 AN: 68012

Other (OTH) AF: 0.0194 AC: 41 AN: 2112

Alfa AF: 0.0274 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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs17101915; hg19: chr14-65001950;