7-76626174-C-T

Variant names:

• chr7-76626174-C-T
• rs1056119
• ENST00000418663.5:n.859C>T

Variant summary

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

The ENST00000418663.5(LINC03009):​n.859C>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 0.355 in 1,584,220 control chromosomes in the GnomAD database, including 102,505 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 0.37 (10532 hom., cov: 30)
  • Exomes 𝑓: 0.35 (91973 hom.)
• Consequence: LINC03009 ENST00000418663.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 4 publications found

Genes affected

LINC03009 (HGNC:56134): (long intergenic non-protein coding RNA 3009)

POMZP3 (HGNC:9203): (POM121 and ZP3 fusion) This gene appears to have resulted from a fusion of DNA sequences derived from 2 distinct loci, specifically through the duplication of two internal exons from the POM121 gene and four 3' exons from the ZP3 gene. The 5' end of this gene is similar to the 5` coding region of the POM121 gene which encodes an integral nuclear pore membrane protein. However, the protein encoded by this gene lacks the nuclear pore localization motif. The 3' end of this gene is similar to the last 4 exons of the zona pellucida glycoprotein 3 (ZP3) gene and the encoded protein retains one zona pellucida domain. Multiple protein isoforms are encoded by transcript variants of this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POMZP3	NM_012230.5	c.-110G>A		5_prime_UTR_variant	Exon 2 of 7	ENST00000310842.9	NP_036362.3
LINC03009	NR_029411.1	n.878C>T		non_coding_transcript_exon_variant	Exon 3 of 3
POMZP3	NM_152992.4	c.-110G>A		5_prime_UTR_variant	Exon 2 of 5		NP_694537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POMZP3	ENST00000310842.9	c.-110G>A		5_prime_UTR_variant	Exon 2 of 7	1	NM_012230.5	ENSP00000309233.4

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55713 AN: 151464 Hom.: 10516 Cov.: 30

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.400

GnomAD4 exome AF: 0.354 AC: 506817 AN: 1432644 Hom.: 91973 Cov.: 40 AF XY: 0.353 AC XY: 251010 AN XY: 710682

African (AFR) AF: 0.454 AC: 14784 AN: 32558

American (AMR) AF: 0.265 AC: 10632 AN: 40082

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 9311 AN: 25600

East Asian (EAS) AF: 0.151 AC: 5787 AN: 38210

South Asian (SAS) AF: 0.325 AC: 27059 AN: 83386

European-Finnish (FIN) AF: 0.258 AC: 13385 AN: 51938

Middle Eastern (MID) AF: 0.492 AC: 2814 AN: 5724

European-Non Finnish (NFE) AF: 0.367 AC: 401745 AN: 1095810

Other (OTH) AF: 0.359 AC: 21300 AN: 59336

GnomAD4 genome AF: 0.368 AC: 55755 AN: 151576 Hom.: 10532 Cov.: 30 AF XY: 0.362 AC XY: 26788 AN XY: 74090

African (AFR) AF: 0.454 AC: 18703 AN: 41214

American (AMR) AF: 0.313 AC: 4770 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3466

East Asian (EAS) AF: 0.185 AC: 951 AN: 5154

South Asian (SAS) AF: 0.312 AC: 1498 AN: 4804

European-Finnish (FIN) AF: 0.236 AC: 2483 AN: 10524

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.364 AC: 24728 AN: 67872

Other (OTH) AF: 0.404 AC: 849 AN: 2102

Alfa AF: 0.153 Hom.: 187

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	16
DANN	Benign	0.96
PhyloP100		1.2
PromoterAI		-0.055	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=297/3	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1056119; hg19: chr7-76255491; COSMIC: COSV51885371; COSMIC: COSV51885371;