rs369159546

Variant names:

• chr6-43524804-TCCTTCCCCCATG-T
• rs369159546
• NM_020750.3:c.3312+15_3312+26delCATGGGGGAAGG

Your query was ambiguous. Multiple possible variants found:

• chr6-43524804-TCCTTCCCCCATG-T
• chr6-43524804-TCCTTCCCCCATG-TCCTTCCCCCATGCCTTCCCCCATG
• chr6-43524804-TCCTTCCCCCATG-TCCTTCCCCCATGCCTTCCCCCCCTTCCCCCATG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_020750.3(XPO5):​c.3312+15_3312+26delCATGGGGGAAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: XPO5 NM_020750.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

XPO5 (HGNC:17675): (exportin 5) This gene encodes a member of the karyopherin family that is required for the transport of small RNAs and double-stranded RNA-binding proteins from the nucleus to the cytoplasm. The encoded protein translocates cargo through the nuclear pore complex in a RanGTP-dependent process. [provided by RefSeq, Aug 2011]

POLR1C (HGNC:20194): (RNA polymerase I and III subunit C) The protein encoded by this gene is a subunit of both RNA polymerase I and RNA polymerase III complexes. The encoded protein is part of the Pol core element. Mutations in this gene have been associated with Treacher Collins syndrome (TCS) and hypomyelinating leukodystrophy 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XPO5	NM_020750.3	c.3312+15_3312+26delCATGGGGGAAGG		intron_variant	Intron 30 of 31	ENST00000265351.12	NP_065801.1
POLR1C	NM_001318876.2	c.922+3765_922+3776delCATGCCTTCCCC		intron_variant	Intron 8 of 8		NP_001305805.1
POLR1C	NM_001363658.2	c.922+3765_922+3776delCATGCCTTCCCC		intron_variant	Intron 8 of 9		NP_001350587.1
XPO5	NR_144392.2	n.3624+15_3624+26delCATGGGGGAAGG		intron_variant	Intron 31 of 32

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XPO5	ENST00000265351.12	c.3312+15_3312+26delCATGGGGGAAGG		intron_variant	Intron 30 of 31	1	NM_020750.3	ENSP00000265351.7

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs369159546; hg19: chr6-43492542;