chr6-149731629-C-T

Variant names:

• chr6-149731629-C-T
• rs61756083
• NM_198887.3:c.897G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_198887.3(NUP43):​c.897G>A​(p.Ser299Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000948 in 1,612,170 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0011 (1 hom., cov: 31)
  • Exomes 𝑓: 0.00093 (8 hom.)
• Consequence: NUP43 NM_198887.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.115
• Publications: 3 publications found

Genes affected

NUP43 (HGNC:21182): (nucleoporin 43) Bidirectional transport of macromolecules between the cytoplasm and nucleus occurs through nuclear pore complexes (NPCs) embedded in the nuclear envelope. NPCs are composed of subcomplexes, and NUP43 is part of one such subcomplex, Nup107-160 (Loiodice et al., 2004 [PubMed 15146057]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BP6: Variant 6-149731629-C-T is Benign according to our data. Variant chr6-149731629-C-T is described in ClinVar as Benign. ClinVar VariationId is 778010.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.115 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 8 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198887.3. 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
	NUP43	NM_198887.3	MANE Select	c.897G>A	p.Ser299Ser	synonymous	Exon 7 of 8	NP_942590.1	Q8NFH3-1
	NUP43	NR_104456.2		n.931G>A		non_coding_transcript_exon	Exon 7 of 9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP43	ENST00000340413.7	TSL:1 MANE Select	c.897G>A	p.Ser299Ser	synonymous	Exon 7 of 8	ENSP00000342262.2	Q8NFH3-1
	NUP43	ENST00000917625.1		c.897G>A	p.Ser299Ser	synonymous	Exon 7 of 9	ENSP00000587684.1
	NUP43	ENST00000917622.1		c.897G>A	p.Ser299Ser	synonymous	Exon 8 of 9	ENSP00000587681.1

Frequencies

GnomAD3 genomes AF: 0.00110 AC: 166 AN: 151054 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000268

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.00132

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000625

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0321

Gnomad NFE AF: 0.000781

Gnomad OTH AF: 0.00193

GnomAD2 exomes AF: 0.00138 AC: 347 AN: 251126 AF XY: 0.00155

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.00101

Gnomad ASJ exome AF: 0.0168

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000933

Gnomad OTH exome AF: 0.00342

GnomAD4 exome AF: 0.000932 AC: 1362 AN: 1461044 Hom.: 8 Cov.: 32 AF XY: 0.000985 AC XY: 716 AN XY: 726836

African (AFR) AF: 0.000807 AC: 27 AN: 33450

American (AMR) AF: 0.00110 AC: 49 AN: 44634

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 452 AN: 26100

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39654

South Asian (SAS) AF: 0.000418 AC: 36 AN: 86210

European-Finnish (FIN) AF: 0.0000562 AC: 3 AN: 53354

Middle Eastern (MID) AF: 0.0125 AC: 72 AN: 5766

European-Non Finnish (NFE) AF: 0.000517 AC: 575 AN: 1111534

Other (OTH) AF: 0.00244 AC: 147 AN: 60342

GnomAD4 genome AF: 0.00111 AC: 167 AN: 151126 Hom.: 1 Cov.: 31 AF XY: 0.00106 AC XY: 78 AN XY: 73690

African (AFR) AF: 0.000267 AC: 11 AN: 41144

American (AMR) AF: 0.00132 AC: 20 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5110

South Asian (SAS) AF: 0.00105 AC: 5 AN: 4782

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10284

Middle Eastern (MID) AF: 0.0310 AC: 9 AN: 290

European-Non Finnish (NFE) AF: 0.000781 AC: 53 AN: 67874

Other (OTH) AF: 0.00191 AC: 4 AN: 2090

Alfa AF: 0.00213 Hom.: 0

Bravo AF: 0.00118

EpiCase AF: 0.00185

EpiControl AF: 0.00261

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	7.0
DANN	Benign	0.64
PhyloP100		-0.12
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=95/5	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs61756083; hg19: chr6-150052765;