ENST00000701551.1:n.22G>T

Variant names:

• chr10-75276189-G-T
• rs11001359
• ENST00000701551.1:n.22G>T

Variant summary

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

The ENST00000701551.1(ZNF503-AS1):​n.22G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,050 control chromosomes in the GnomAD database, including 15,192 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 0.42 (15192 hom., cov: 32)
• Consequence: ZNF503-AS1 ENST00000701551.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 2 publications found

Genes affected

ZNF503-AS1 (HGNC:27370): (ZNF503 antisense RNA 1)

HMGA1P5 (HGNC:19120): (high mobility group AT-hook 1 pseudogene 5)

ENSG00000270087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HMGA1P5		n.75276189G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF503-AS1	ENST00000701551.1	n.22G>T		non_coding_transcript_exon_variant	Exon 1 of 6
ZNF503-AS1	ENST00000701852.1	n.13G>T		non_coding_transcript_exon_variant	Exon 1 of 1
ZNF503-AS1	ENST00000734871.1	n.34G>T		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64405 AN: 151932 Hom.: 15163 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.424 AC: 64480 AN: 152050 Hom.: 15192 Cov.: 32 AF XY: 0.419 AC XY: 31164 AN XY: 74314

African (AFR) AF: 0.624 AC: 25860 AN: 41474

American (AMR) AF: 0.341 AC: 5212 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1407 AN: 3468

East Asian (EAS) AF: 0.176 AC: 902 AN: 5136

South Asian (SAS) AF: 0.529 AC: 2553 AN: 4826

European-Finnish (FIN) AF: 0.234 AC: 2478 AN: 10598

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24681 AN: 67944

Other (OTH) AF: 0.440 AC: 928 AN: 2108

Alfa AF: 0.393 Hom.: 2588

Bravo AF: 0.433

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.50
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs11001359; hg19: chr10-77035947; COSMIC: COSV69398133;