19-23269280-G-A

Variant names:

• chr19-23269280-G-A
• rs295424
• ENST00000611392.5:c.-212+938C>T

Variant summary

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

The ENST00000611392.5(ENSG00000283201):​c.-212+938C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,370 control chromosomes in the GnomAD database, including 19,067 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 0.48 (19065 hom., cov: 29)
  • Exomes 𝑓: 0.27 (2 hom.)
• Consequence: ENSG00000283201 ENST00000611392.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 2 publications found

Genes affected

ENSG00000283201 (HGNC:):

IPO5P1 (HGNC:49687): (importin 5 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611392.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPO5P1	NR_103741.1		n.251+938C>T		intron	N/A
	IPO5P1	NR_103742.1		n.176+4796C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283201	ENST00000611392.5	TSL:5	c.-212+938C>T		intron	N/A	ENSP00000478939.2	A0A087WUU8
	ENSG00000284428	ENST00000640920.1	TSL:3	n.807C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000269107	ENST00000594653.1	TSL:5	n.232+938C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72593 AN: 151224 Hom.: 19049 Cov.: 29

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 0.269 AC: 7 AN: 26 Hom.: 2 Cov.: 0 AF XY: 0.208 AC XY: 5 AN XY: 24

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.227 AC: 5 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00000907115), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.480 AC: 72620 AN: 151344 Hom.: 19065 Cov.: 29 AF XY: 0.488 AC XY: 36046 AN XY: 73920

African (AFR) AF: 0.252 AC: 10410 AN: 41320

American (AMR) AF: 0.615 AC: 9339 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1889 AN: 3452

East Asian (EAS) AF: 0.688 AC: 3516 AN: 5114

South Asian (SAS) AF: 0.573 AC: 2744 AN: 4788

European-Finnish (FIN) AF: 0.608 AC: 6346 AN: 10442

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36721 AN: 67746

Other (OTH) AF: 0.489 AC: 1027 AN: 2102

Alfa AF: 0.493 Hom.: 2414

Bravo AF: 0.473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.32
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs295424; hg19: chr19-23452082;